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Дата изменения: Unknown
Дата индексирования: Sat Apr 9 22:36:54 2016
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Best resolution Pfam family representatives
The work is supported by the Russian Foundation for Basic Research, grant 10-07-00685-a

Best resolution Pfam family representatives bound with nucleic acid

Full collection of domains with contacting nucleic acids structures is available at http://mouse.belozersky.msu.ru/npidb/pdb/samples

Family Code Domain NA Resolution
TIG (IPT/TIG domain) 1A3Q A:228-325 dna 2.1
RHD (Rel homology domain (RHD)) 1A3Q B:40-220 dna 2.1
zf-C2H2 (Zinc finger, C2H2 type) 1AAY A:163-185 dna 1.6
TFIIB (Transcription factor TFIIB repeat) 1AIS B:1212-1282 dna 2.1
RIP (Ribosome inactivating protein) 1APG A:6-263 rna 3
PARP_regulatory (Poly A polymerase regulatory subunit) 1AV6 A:4-296 rna 2.8
RHH_1 (Ribbon-helix-helix protein, copG family) 1B01 B:4-42 dna 2.56
GTP_EFTU_D3 (Elongation factor Tu C-terminal domain) 1B23 P:311-405 rna 2.6
GTP_EFTU_D2 (Elongation factor Tu domain 2) 1B23 P:236-306 rna 2.6
GTP_EFTU (Elongation factor Tu GTP binding domain) 1B23 P:10-213 rna 2.6
EBV-NA1 (Epstein Barr virus nuclear antigen-1, DNA-binding domain) 1B3T B:461-606 dna 2.2
Ets (Ets-domain) 1BC7 C:4-87 dna 2.01
Arc (Arc-like DNA binding domain) 1BDT A:4-52 dna 2.5
STAT_bind (STAT protein, DNA binding domain) 1BF5 A:317-567 dna 2.9
HTH_AraC (Bacterial regulatory helix-turn-helix proteins, AraC family) 1BL0 A:67-111 dna 2.3
tRNA_anti (OB-fold nucleic acid binding domain) 1C0A A:18-102 rna 2.4
tRNA-synt_2 (tRNA synthetases class II (D, K and N)) 1C0A A:117-559 rna 2.4
7kD_DNA_binding (7kD DNA-binding domain) 1C8C A:3-64 dna 1.45
EcoRI (Restriction endonuclease EcoRI) 1CL8 A:18-274 dna 1.8
PD-C2-AF1 (POU domain, class 2, associating factor 1) 1CQT I:285-328 dna 3.2
Vsr (DNA mismatch endonuclease Vsr) 1CW0 A:3-77 dna 2.3
Bromo_coat (Bromovirus coat protein) 1CWP A:42-190 rna 3.2
Zn_clus (Fungal Zn(2)-Cys(6) binuclear cluster domain) 1D66 A:9-47 dna 2.7
Gal4_dimer (Gal4-like dimerisation domain) 1D66 A:50-64 dna 2.7
3_5_exonuc (3'-5' exonuclease) 1D8Y A:330-517 dna 2.08
Tymo_coat (Tymovirus coat protein) 1DDL B:7-178 rna 2.7
Endonuc-BglII (Restriction endonuclease BglII) 1DFM B:6-170 dna 1.5
zf-C4 (Zinc finger, C4 type (two domains)) 1DSZ A:1133-1208 dna 1.7
Pou (Pou domain - N-terminal to homeobox domain) 1E3O C:1-75 dna 1.9
Homeobox (Homeobox domain) 1E3O C:102-158 dna 1.9
SRP14 (Signal recognition particle 14kD protein) 1E8O B:4-94 rna 3.2
SRP9 (Signal recognition particle 9 kDa protein (SRP9)) 1E8O A:3-77 rna 3.2
HhH-GPD (HhH-GPD superfamily base excision DNA repair protein) 1EBM A:142-302 dna 2.1
HHH (Helix-hairpin-helix motif) 1EBM A:228-257 dna 2.1
KH_1 (KH domain) 1EC6 B:7-72 rna 2.4
SRF-TF (SRF-type transcription factor (DNA-binding and dimerisation domain)) 1EGW C:9-59 dna 1.5
UDG (Uracil DNA glycosylase superfamily) 1EMH A:130-292 dna 1.8
Endonuc-EcoRV (Restriction endonuclease EcoRV) 1EON B:6-245 dna 1.6
Histone (Core histone H2A/H2B/H3/H4) 1EQZ A:18-91 dna 2.5
Pur_DNA_glyco (Methylpurine-DNA glycosylase (MPG)) 1EWN A:87-284 dna 2.1
Phage_integrase (Phage integrase family) 1F44 A:145-334 dna 2.05
Arg_tRNA_synt_N (Arginyl tRNA synthetase N terminal domain) 1F7U A:33-114 rna 2.2
DALR_1 (DALR anticodon binding domain) 1F7U A:489-607 rna 2.2
tRNA-synt_1d (tRNA synthetases class I (R)) 1F7U A:123-475 rna 2.2
Anticodon_1 (Anticodon-binding domain) 1FFY A:678-832 rna 2.2
tRNA-synt_1 (tRNA synthetases class I (I, L, M and V)) 1FFY A:26-634 rna 2.2
Flp_C (Recombinase Flp protein) 1FLO A:136-380 dna 2.65
Flp_N (Recombinase Flp protein N-terminus) 1FLO A:44-128 dna 2.65
FokI_N (Restriction endonuclease FokI, recognition domain) 1FOK A:4-143 dna 2.8
Endonuc-FokI_C (Restriction endonuclease FokI, C terminal) 1FOK A:387-579 dna 2.8
FokI_C (Restriction endonuclease FokI, catalytic domain) 1FOK A:146-281 dna 2.8
Ribosomal_S15 (Ribosomal protein S15) 1G1X B:6-78 rna 2.6
Ribosomal_S6 (Ribosomal protein S6) 1G1X A:2-93 rna 2.6
Ribosomal_S18 (Ribosomal protein S18) 1G1X C:27-80 rna 2.6
LAGLIDADG_1 (LAGLIDADG endonuclease) 1G9Z B:213-311 dna 1.8
bZIP_1 (bZIP transcription factor) 1GD2 F:74-137 dna 2
TrpBP (Tryptophan RNA-binding attenuator protein) 1GTF V:1-74 rna 1.75
bZIP_2 (Basic region leucine zipper) 1GU5 B:270-323 dna 2.1
VP40 (Matrix protein VP40) 1H2D A:31-212 rna 2.6
tRNA-synt_1b (tRNA synthetases class I (W and Y)) 1H3E A:33-318 rna 2.9
T-box (T-box) 1H6F A:104-286 dna 1.7
Runt (Runt domain) 1HJB C:60-182 dna 3
CenpB-DNA-bind (Centromere binding protein B, DNA binding) 1HLV A:68-129 dna 2.5
CENP-B_N (CENP-B N-terminal DNA-binding domain) 1HLV A:2-56 dna 2.5
NUMOD3 (NUMOD3 motif) 1I3J A:178-191 dna 2.2
RNA_pol_Rpb1_5 (RNA polymerase Rpb1, domain 5) 1I6H A:807-1398 dna 3.3
RNA_pol_Rpb2_7 (RNA polymerase Rpb2, domain 7) 1I6H B:1126-1219 dna 3.3
RNA_pol_Rpb1_2 (RNA polymerase Rpb1, domain 2) 1I6H A:342-507 dna 3.3
RNA_pol_Rpb2_6 (RNA polymerase Rpb2, domain 6) 1I6H B:750-1124 dna 3.3
RNA_pol_Rpb1_1 (RNA polymerase Rpb1, domain 1) 1I6H A:11-340 dna 3.3
RNA_pol_Rpb2_3 (RNA polymerase Rpb2, domain 3) 1I6H B:481-546 rna 3.3
Ribosomal_S8 (Ribosomal protein S8) 1I6U B:5-130 rna 2.6
NaeI (Restriction endonuclease NaeI) 1IAW B:12-309 dna 2.4
HNF-1_N (Hepatocyte nuclear factor 1 (HNF-1), N terminus) 1IC8 B:85-176 dna 2.6
DNA_pol_B (DNA polymerase family B) 1IG9 A:391-859 dna 2.6
DNA_pol_B_exo (DNA polymerase family B, exonuclease domain) 1IG9 A:19-293 dna 2.6
Ribosomal_S7 (Ribosomal protein S7p/S5e) 1J5E G:2-150 rna 3.05
Ribosomal_S10 (Ribosomal protein S10p/S20e) 1J5E J:4-99 rna 3.05
Ribosomal_S19 (Ribosomal protein S19) 1J5E S:4-84 rna 3.05
Ribosomal_S14 (Ribosomal protein S14p/S29e) 1J5E N:7-61 rna 3.05
Ribosomal_S5_C (Ribosomal protein S5, C-terminal domain) 1J5E E:81-154 rna 3.05
Ribosomal_S13 (Ribosomal protein S13/S18) 1J5E M:4-110 rna 3.05
Ribosomal_S9 (Ribosomal protein S9/S16) 1J5E I:8-128 rna 3.05
Ribosomal_S17 (Ribosomal protein S17) 1J5E Q:9-77 rna 3.05
S4 (S4 domain) 1J5E D:100-147 rna 3.05
Ribosomal_S5 (Ribosomal protein S5, N-terminal domain) 1J5E E:6-72 rna 3.05
Ribosomal_S12 (Ribosomal protein S12) 1J5E L:6-127 rna 3.05
Ribosomal_S20p (Ribosomal protein S20) 1J5E T:8-91 rna 3.05
Ribosomal_S16 (Ribosomal protein S16) 1J5E P:8-67 rna 3.05
Ribosomal_S4 (Ribosomal protein S4/S9 N-terminal domain) 1J5E D:3-99 rna 3.05
Ribosomal_S11 (Ribosomal protein S11) 1J5E K:18-127 rna 3.05
Ribosomal_S2 (Ribosomal protein S2) 1J5E B:11-227 rna 3.05
TEBP_beta (Telomere-binding protein beta subunit (TEBP beta)) 1JB7 B:1-260 dna 1.86
HTH_7 (Helix-turn-helix domain of resolvase) 1JKR C:139-183 dna 2.28
IMS (impB/mucB/samB family) 1JX4 A:6-342 dna 1.7
Topoisom_I_N (Eukaryotic DNA topoisomerase I, DNA binding fragment) 1K4T A:215-429 dna 2.1
Topoisom_I (Eukaryotic DNA topoisomerase I, catalytic core) 1K4T A:432-673 dna 2.1
PPV_E1_C (Papillomavirus helicase) 1KSY B:166-309 dna 3.05
GerE (Bacterial regulatory proteins, luxR family) 1L3L D:171-228 dna 1.66
DNA_pol_A (DNA polymerase family A) 1L3V A:495-875 dna 1.71
HTH_3 (Helix-turn-helix) 1LMB 3:22-77 dna 1.8
SRP19 (SRP19 protein) 1LNG A:1-87 rna 2.3
LSM (LSM domain) 1M8V A:107-172 rna 2.6
MH1 (MH1 domain) 1MHD B:28-131 dna 2.8
MetJ (Met Apo-repressor, MetJ) 1MJO B:2-104 dna 2.1
Transposase_11 (Transposase DDE domain) 1MM8 A:130-363 dna 2.8
Transposase_Tn5 (Transposase Tn5 dimerisation domain) 1MM8 A:368-476 dna 2.8
NDT80_PhoG (NDT80 / PhoG like DNA-binding family) 1MNN A:105-334 dna 1.4
Parvo_coat (Parvovirus coat protein VP2) 1MVM A:39-569 dna 3.5
Ribosomal_L1 (Ribosomal protein L1p/L10e family) 1MZP A:3-212 rna 2.65
RdRP_5 (Reovirus RNA-dependent RNA polymerase lambda 3) 1N38 A:1-1263 rna 2.8
tRNA-synt_1c (tRNA synthetases class I (E and Q), catalytic domain) 1N78 B:1-312 rna 2.1
RnaseA (Pancreatic ribonuclease) 1OJ8 A:2-102 dna 1.7
SmpB (SmpB protein) 1P6V C:5-75 rna 3.2
Bac_DNA_binding (Bacterial DNA-binding protein) 1P71 A:1-90 dna 1.9
PAX ('Paired box' domain) 1PDN C:2-124 dna 2.5
H2TH (Formamidopyrimidine-DNA glycosylase H2TH domain) 1PJI A:132-224 dna 1.9
zf-FPG_IleRS (Zinc finger found in FPG and IleRS) 1PJI A:243-271 dna 1.9
Fapy_DNA_glyco (Formamidopyrimidine-DNA glycosylase N-terminal domain) 1PJI A:2-116 dna 1.9
RNA_pol (DNA-dependent RNA polymerase) 1QLN A:449-883 dna 2.4
TBP (Transcription factor TFIID (or TATA-binding protein, TBP)) 1QN4 A:110-196 dna 1.86
HMG_box (HMG (high mobility group) box) 1QRV B:5-71 dna 2.2
tRNA-synt_1c_C (tRNA synthetases class I (E and Q), anti-codon binding domain) 1QTQ A:340-528 rna 2.25
AP_endonuc_2 (Xylose isomerase-like TIM barrel) 1QUM A:18-239 dna 1.55
SRP54_N (SRP54-type protein, helical bundle domain) 1QZW A:1-83 rna 4.1
SRP_SPB (Signal peptide binding domain) 1QZW A:326-428 rna 4.1
RVT_thumb (Reverse transcriptase thumb domain) 1R0A A:239-308 dna 2.8
RVT_connect (Reverse transcriptase connection domain) 1R0A A:318-420 dna 2.8
RnaseH (RNase H) 1R0A A:436-558 dna 2.8
TruB_N (TruB family pseudouridylate synthase (N terminal domain)) 1R3E A:33-201 rna 2.1
PUA (PUA domain) 1R3E A:239-309 rna 2.1
MerR (MerR family regulatory protein) 1R8E A:7-45 dna 2.4
Tyr-DNA_phospho (Tyrosyl-DNA phosphodiesterase) 1RFF A:159-582 dna 1.7
Sigma70_r4 (Sigma-70, region 4) 1RIO H:372-425 dna 2.3
Ribonuclease (ribonuclease) 1RNB A:20-109 dna 1.9
XPG_N (XPG N-terminal domain) 1RXV B:13-101 dna 2.5
Rep_N (Rep protein catalytic domain like) 1RZ9 E:4-189 dna 3.1
Seryl_tRNA_N (Seryl-tRNA synthetase N-terminal domain) 1SER B:501-605 rna 2.9
tRNA-synt_2b (tRNA synthetase class II core domain (G, H, P, S and T)) 1SER B:668-840 rna 2.9
z-alpha (Adenosine deaminase z-alpha domain) 1SFU A:30-70 dna 2
T4-Gluco-transf (Bacteriophage T4 beta-glucosyltransferase) 1SXP B:1-38 dna 2.5
IRF (Interferon regulatory factor transcription factor) 1T2K A:7-112 dna 3
Thioredoxin (Thioredoxin) 1T8E B:4-107 dna 2.54
Trp_repressor (Trp repressor protein) 1TRR J:18-105 dna 2.4
P53 (P53 DNA-binding domain) 1TSR C:96-289 dna 2.2
LAG1-DNAbind (LAG1, DNA binding) 1TTU A:216-380 dna 2.85
Beta-trefoil (Beta-trefoil) 1TTU A:384-536 dna 2.85
Endonuc-HincII (Restriction endonuclease HincII) 1TX3 C:3-258 dna 2.5
DALR_2 (DALR domain) 1U0B B:341-402 rna 2.3
tRNA-synt_1e (tRNA synthetases class I (C) catalytic domain) 1U0B B:14-314 rna 2.3
RRM_1 (RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)) 1U1K A:17-87 dna 2
Transposase_5 (Transposase) 1U78 A:66-134 dna 2.69
Fe_dep_repress (Iron dependent repressor, N-terminal DNA binding domain) 1U8R D:3-63 dna 2.75
RdRP_1 (RNA dependent RNA polymerase) 1UVM A:21-638 rna 2
HNH (HNH endonuclease) 1V15 A:88-134 dna 2.4
Ribosomal_L14 (Ribosomal protein L14p/L23e) 1VQO K:11-132 rna 2.2
Ribosomal_L5_C (ribosomal L5P family C-terminus) 1VQO D:69-167 rna 2.2
Ribosomal_L21e (Ribosomal protein L21e) 1VQO Q:2-95 rna 2.2
Ribosomal_L30 (Ribosomal protein L30p/L7e) 1VQO W:1-52 rna 2.2
Ribosomal_L37e (Ribosomal protein L37e) 1VQO 1:3-56 rna 2.2
Ribosomal_L18p (Ribosomal L18p/L5e family) 1VQO N:10-130 rna 2.2
Ribosomal_L13 (Ribosomal protein L13) 1VQO J:9-119 rna 2.2
Ribosomal_L5 (Ribosomal protein L5) 1VQO D:12-65 rna 2.2
Ribosomal_L3 (Ribosomal protein L3) 1VQO B:46-313 rna 2.2
Ribosomal_L37ae (Ribosomal L37ae protein family) 1VQO Z:11-92 rna 2.2
Ribosomal_L16 (Ribosomal protein L16p/L10e) 1VQO H:2-163 rna 2.2
Ribosomal_L24e (Ribosomal protein L24e) 1VQO U:2-66 rna 2.2
L15 (Ribosomal protein L15) 1VQO O:64-95 rna 2.2
Ribosomal_L32e (Ribosomal protein L32) 1VQO Y:125-232 rna 2.2
Ribosomal_L44 (Ribosomal protein L44) 1VQO 3:16-92 rna 2.2
Ribosomal_L2 (Ribosomal Proteins L2, RNA binding domain) 1VQO A:11-83 rna 2.2
Ribosomal_L2_C (Ribosomal Proteins L2, C-terminal domain) 1VQO A:89-222 rna 2.2
Ribosomal_L15e (Ribosomal L15) 1VQO M:4-193 rna 2.2
Ribosomal_L7Ae (Ribosomal protein L7Ae/L30e/S12e/Gadd45 family) 1VQO F:15-109 rna 2.2
Ribosomal_L23 (Ribosomal protein L23) 1VQO S:3-82 rna 2.2
KOW (KOW motif) 1VQO T:45-76 rna 2.2
Ribosomal_L31e (Ribosomal protein L31e) 1VQO X:2-91 rna 2.2
Ribosomal_L11 (Ribosomal protein L11, RNA binding domain) 1VQO I:72-140 rna 2.2
Ribosomal_L4 (Ribosomal protein L4/L1 family) 1VQO C:14-246 rna 2.2
Ribosomal_L19e (Ribosomal protein L19e) 1VQO P:2-148 rna 2.2
Ribosomal_L29 (Ribosomal L29 protein) 1VQO V:6-64 rna 2.2
Ribosomal_L6 (Ribosomal protein L6) 1VQO E:8-80 rna 2.2
Ribosomal_L22 (Ribosomal protein L22p/L17e) 1VQO R:17-150 rna 2.2
Ribosomal_L10 (Ribosomal protein L10) 1VQO G:11-110 rna 2.2
Ribosomal_L39 (Ribosomal L39 protein) 1VQO 2:8-49 rna 2.2
Myb_DNA-binding (Myb-like DNA-binding domain) 1W0U B:447-495 dna 1.8
MutS_I (MutS domain I) 1WB9 B:11-123 dna 2.1
MutS_IV (MutS family domain IV) 1WB9 B:428-519 dna 2.1
MutS_III (MutS domain III) 1WB9 B:264-564 dna 2.1
HutP (HutP) 1WPU A:9-148 rna 1.48
DNA_pol_B_2 (DNA polymerase type B, organellar and viral) 1XI1 A:53-488 dna 2.2
Telo_bind (Telomere-binding protein alpha subunit, central domain) 1XJV A:39-141 dna 1.73
Ribosomal_S3_N (Ribosomal protein S3, N-terminal domain) 1XMO C:2-63 rna 3.25
Ribosomal_S3_C (Ribosomal protein S3, C-terminal domain) 1XMO C:120-203 rna 3.25
Ribosomal_L27 (Ribosomal L27 protein) 1Y69 U:2-82 rna 3.33
MethyltransfD12 (D12 class N6 adenine-specific DNA methyltransferase) 1YF3 B:7-241 dna 2.29
DNA_binding_1 (6-O-methylguanine DNA methyltransferase, DNA binding domain) 1YFH A:92-177 dna 3.01
Endonuc-MspI (Restriction endonuclease MspI) 1YFI B:2-262 dna 2.7
TROVE (TROVE domain) 1YVP B:16-369 rna 2.2
dsrm (Double-stranded RNA binding motif) 1YYW C:152-217 rna 2.8
RVT_1 (Reverse transcriptase (RNA-dependent DNA polymerase)) 1ZTW A:92-273 dna 1.8
ParB (ParB family) 1ZX4 A:199-325 dna 2.98
CAF1 (CAF1 family ribonuclease) 2A1R A:1-392 rna 2.6
Ribosomal_L34 (Ribosomal protein L34) 2AW4 2:1-44 rna 3.46
Ribosomal_L25p (Ribosomal L25p family) 2AW4 V:4-91 rna 3.46
Ribosomal_L33 (Ribosomal protein L33) 2AW4 1:6-53 rna 3.46
Ribosomal_L20 (Ribosomal protein L20) 2AW4 Q:2-109 rna 3.46
Ribosomal_L9_N (Ribosomal protein L9, N-terminal domain) 2AW4 H:1-48 rna 3.46
Ribosomal_L11_N (Ribosomal protein L11, N-terminal domain) 2AW4 I:8-67 rna 3.46
Ribosomal_L36 (Ribosomal protein L36) 2AW4 4:1-38 rna 3.46
Ribosomal_L35p (Ribosomal protein L35) 2AW4 3:4-62 rna 3.46
Ribosomal_L15 (Ribosomal protein L15 amino terminal region) 2AW4 L:1-101 rna 3.46
Ribosomal_L31 (Ribosomal protein L31) 2AW4 Z:1-67 rna 3.46
Ribosomal_L19 (Ribosomal protein L19) 2AW4 P:2-114 rna 3.46
Ribosomal_S21 (Ribosomal protein S21) 2AW7 U:2-55 rna 3.46
RNA_pol_Rpb2_1 (RNA polymerase beta subunit) 2B63 B:42-464 rna 3.8
Piwi (Piwi domain) 2BGG B:110-406 rna 2.2
Microvir_J (Microvirus J protein) 2BPA 3:2-37 dna 3
Phage_F (Capsid protein (F protein)) 2BPA 1:2-425 dna 3
S1 (S1 RNA binding domain) 2C0B L:35-119 rna 3.18
Levi_coat (Levivirus coat protein) 2C4Q A:3-129 rna 2.38
DNA_methylase (C-5 cytosine-specific DNA methylase) 2C7O A:12-320 dna 1.9
cNMP_binding (Cyclic nucleotide-binding domain) 2CGP A:20-111 dna 2.2
Crp (Bacterial regulatory proteins, crp family) 2CGP A:165-196 dna 2.2
tRNA-synt_1g (tRNA synthetases class I (M)) 2CT8 A:7-359 rna 2.7
Pencillinase_R (Penicillinase repressor) 2D45 B:8-122 dna 3.8
LacI (Bacterial regulatory proteins, lacI family) 2PUE A:3-28 dna 2.7
Endonuc-PvuII (Restriction endonuclease PvuII) 2PVI A:3-157 dna 1.76
BamHI (Restriction endonuclease BamHI) 3BAM A:1-168 dna 1.8
HSF_DNA-bind (HSF-type DNA-binding) 3HTS B:195-281 dna 1.75
Cro (Cro) 3ORC A:2-56 dna 3

231 rows shown

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