eF-site ID 1ih7-A
PDB Code 1ih7
Chain A

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Title High-Resolution Structure of Apo RB69 DNA Polymerase
Classification TRANSFERASE
Compound DNA POLYMERASE
Source Enterobacteria phage RB69 (Bacteriophage RB69) (DPOL_BPR69)
Sequence A:  MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAH
CPESQATKYFDIYGKPCTRKLFANMRDASQWIKRMEDIGL
EALGMDDFKLAYLSDTYNYEIKYDHTKIRVANFDIEVTSP
DGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVE
EWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLME
YLNFWQQKTPVILTGWNVESFDIPYVYNRIKNIFGESTAK
RLSPHRKTRVKVIENMYGSREIITLFGISVLDYIDLYKKF
SFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRY
ISYNIIDVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFS
PIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPI
PNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLH
DYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFN
QRKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRF
DFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRK
LLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERK
VNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESK
FRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHL
MFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRY
AEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESL
QEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPK
CPFHIRGILTYNRAIPQVVEGEKVYVLPLREGNPFGDKCI
AWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSA
AKLDYEKKASLFDMFDF
Description


Functional site

1) chain A
residue 327
type
sequence D
description BINDING SITE FOR RESIDUE K A 2002
source : AC1

2) chain A
residue 36
type
sequence S
description BINDING SITE FOR RESIDUE GMP A 1000
source : AC2

3) chain A
residue 38
type
sequence F
description BINDING SITE FOR RESIDUE GMP A 1000
source : AC2

4) chain A
residue 59
type
sequence R
description BINDING SITE FOR RESIDUE GMP A 1000
source : AC2

5) chain A
residue 84
type
sequence G
description BINDING SITE FOR RESIDUE GMP A 1000
source : AC2

6) chain A
residue 85
type
sequence M
description BINDING SITE FOR RESIDUE GMP A 1000
source : AC2

7) chain A
residue 95
type
sequence D
description BINDING SITE FOR RESIDUE GMP A 1000
source : AC2

8) chain A
residue 370
type
sequence F
description BINDING SITE FOR RESIDUE GMP A 1000
source : AC2

9) chain A
residue 374
type
sequence K
description BINDING SITE FOR RESIDUE GMP A 1000
source : AC2

10) chain A
residue 378
type
sequence K
description BINDING SITE FOR RESIDUE GMP A 1000
source : AC2

11) chain A
residue 379
type
sequence V
description BINDING SITE FOR RESIDUE GMP A 1000
source : AC2

12) chain A
residue 380
type
sequence I
description BINDING SITE FOR RESIDUE GMP A 1000
source : AC2

13) chain A
residue 412
type BINDING
sequence L
description BINDING => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:17718515, ECO:0000269|PubMed:21566148, ECO:0000269|PubMed:21923197, ECO:0000305|PubMed:18503083, ECO:0000305|PubMed:23214497, ECO:0000305|PubMed:23921641, ECO:0007744|PDB:2OZM, ECO:0007744|PDB:2OZS, ECO:0007744|PDB:3KD5, ECO:0007744|PDB:3SI6, ECO:0007744|PDB:3SNN, ECO:0007744|PDB:3SPY
source Swiss-Prot : SWS_FT_FI4

14) chain A
residue 619-627
type prosite
sequence YGDTDSIYV
description DNA_POLYMERASE_B DNA polymerase family B signature. YGDTDSIYV
source prosite : PS00116

15) chain A
residue 714
type SITE
sequence D
description Essential for viral replication => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:24116139
source Swiss-Prot : SWS_FT_FI10

16) chain A
residue 621
type SITE
sequence D
description Optimization of metal coordination by the polymerase active site => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000305|PubMed:15057283, ECO:0000305|PubMed:20166752, ECO:0000305|PubMed:22571765, ECO:0000305|PubMed:24116139
source Swiss-Prot : SWS_FT_FI8

17) chain A
residue 706
type SITE
sequence K
description Optimization of metal coordination by the polymerase active site => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:15057283, ECO:0000269|PubMed:22571765
source Swiss-Prot : SWS_FT_FI9

18) chain A
residue 114
type BINDING
sequence D
description BINDING => ECO:0000255|HAMAP-Rule:MF_04100
source Swiss-Prot : SWS_FT_FI1

19) chain A
residue 116
type BINDING
sequence E
description BINDING => ECO:0000255|HAMAP-Rule:MF_04100
source Swiss-Prot : SWS_FT_FI1

20) chain A
residue 222
type BINDING
sequence D
description BINDING => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000305|PubMed:23214497
source Swiss-Prot : SWS_FT_FI2

21) chain A
residue 327
type BINDING
sequence D
description BINDING => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000305|PubMed:23214497
source Swiss-Prot : SWS_FT_FI2

22) chain A
residue 411
type BINDING
sequence D
description BINDING => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:15057283, ECO:0000269|PubMed:17718515, ECO:0000269|PubMed:21566148, ECO:0000269|PubMed:21923197, ECO:0000269|PubMed:22026756, ECO:0000305|PubMed:11389835, ECO:0000305|PubMed:15057282, ECO:0000305|PubMed:18503083, ECO:0000305|PubMed:20166748, ECO:0000305|PubMed:21158418, ECO:0000305|PubMed:22571765, ECO:0000305|PubMed:23214497, ECO:0000305|PubMed:23921641, ECO:0000305|PubMed:24116139, ECO:0007744|PDB:2OZM, ECO:0007744|PDB:2OZS, ECO:0007744|PDB:3KD5, ECO:0007744|PDB:3SI6, ECO:0007744|PDB:3SNN, ECO:0007744|PDB:3SPY
source Swiss-Prot : SWS_FT_FI3

23) chain A
residue 414
type BINDING
sequence S
description BINDING => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0007744|PDB:1IG9, ECO:0007744|PDB:3CFP, ECO:0007744|PDB:3CFR, ECO:0007744|PDB:3CQ8, ECO:0007744|PDB:3LZJ, ECO:0007744|PDB:3NGI, ECO:0007744|PDB:3NHG, ECO:0007744|PDB:3QEP, ECO:0007744|PDB:3QET, ECO:0007744|PDB:3QNO, ECO:0007744|PDB:3RWU, ECO:0007744|PDB:3SQ2, ECO:0007744|PDB:3SQ4, ECO:0007744|PDB:3SUN, ECO:0007744|PDB:3SUO, ECO:0007744|PDB:4DTJ, ECO:0007744|PDB:4DTX, ECO:0007744|PDB:4FJ9, ECO:0007744|PDB:4FJJ, ECO:0007744|PDB:4FJN, ECO:0007744|PDB:4FK2, ECO:0007744|PDB:4J2A, ECO:0007744|PDB:4J2B, ECO:0007744|PDB:4J2D, ECO:0007744|PDB:4J2E, ECO:0007744|PDB:4KHS, ECO:0007744|PDB:4KHU, ECO:0007744|PDB:4KHW, ECO:0007744|PDB:4KHY, ECO:0007744|PDB:4KI4, ECO:0007744|PDB:4KI6, ECO:0007744|PDB:4M3R, ECO:0007744|PDB:4M3T, ECO:0007744|PDB:4M3U, ECO:0007744|PDB:4M3W, ECO:0007744|PDB:4M3X, ECO:0007744|PDB:4M3Y, ECO:0007744|PDB:4M3Z, ECO:0007744|PDB:4M41, ECO:0007744|PDB:4M42, ECO:0007744|PDB:4M45
source Swiss-Prot : SWS_FT_FI5

24) chain A
residue 482
type BINDING
sequence R
description BINDING => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0007744|PDB:1IG9, ECO:0007744|PDB:3CFP, ECO:0007744|PDB:3CFR, ECO:0007744|PDB:3CQ8, ECO:0007744|PDB:3LZJ, ECO:0007744|PDB:3NGI, ECO:0007744|PDB:3NHG, ECO:0007744|PDB:3QEP, ECO:0007744|PDB:3QET, ECO:0007744|PDB:3QNO, ECO:0007744|PDB:3RWU, ECO:0007744|PDB:3SQ2, ECO:0007744|PDB:3SQ4, ECO:0007744|PDB:3SUN, ECO:0007744|PDB:3SUO, ECO:0007744|PDB:4DTJ, ECO:0007744|PDB:4DTX, ECO:0007744|PDB:4FJ9, ECO:0007744|PDB:4FJJ, ECO:0007744|PDB:4FJN, ECO:0007744|PDB:4FK2, ECO:0007744|PDB:4J2A, ECO:0007744|PDB:4J2B, ECO:0007744|PDB:4J2D, ECO:0007744|PDB:4J2E, ECO:0007744|PDB:4KHS, ECO:0007744|PDB:4KHU, ECO:0007744|PDB:4KHW, ECO:0007744|PDB:4KHY, ECO:0007744|PDB:4KI4, ECO:0007744|PDB:4KI6, ECO:0007744|PDB:4M3R, ECO:0007744|PDB:4M3T, ECO:0007744|PDB:4M3U, ECO:0007744|PDB:4M3W, ECO:0007744|PDB:4M3X, ECO:0007744|PDB:4M3Y, ECO:0007744|PDB:4M3Z, ECO:0007744|PDB:4M41, ECO:0007744|PDB:4M42, ECO:0007744|PDB:4M45
source Swiss-Prot : SWS_FT_FI5

25) chain A
residue 560
type BINDING
sequence K
description BINDING => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0007744|PDB:1IG9, ECO:0007744|PDB:3CFP, ECO:0007744|PDB:3CFR, ECO:0007744|PDB:3CQ8, ECO:0007744|PDB:3LZJ, ECO:0007744|PDB:3NGI, ECO:0007744|PDB:3NHG, ECO:0007744|PDB:3QEP, ECO:0007744|PDB:3QET, ECO:0007744|PDB:3QNO, ECO:0007744|PDB:3RWU, ECO:0007744|PDB:3SQ2, ECO:0007744|PDB:3SQ4, ECO:0007744|PDB:3SUN, ECO:0007744|PDB:3SUO, ECO:0007744|PDB:4DTJ, ECO:0007744|PDB:4DTX, ECO:0007744|PDB:4FJJ, ECO:0007744|PDB:4FJN, ECO:0007744|PDB:4FK2, ECO:0007744|PDB:4J2A, ECO:0007744|PDB:4J2B, ECO:0007744|PDB:4J2D, ECO:0007744|PDB:4J2E, ECO:0007744|PDB:4KHS, ECO:0007744|PDB:4KHU, ECO:0007744|PDB:4KHW, ECO:0007744|PDB:4KHY, ECO:0007744|PDB:4KI4, ECO:0007744|PDB:4KI6, ECO:0007744|PDB:4M3R, ECO:0007744|PDB:4M3T, ECO:0007744|PDB:4M3U, ECO:0007744|PDB:4M3W, ECO:0007744|PDB:4M3X, ECO:0007744|PDB:4M3Y, ECO:0007744|PDB:4M3Z, ECO:0007744|PDB:4M41, ECO:0007744|PDB:4M42, ECO:0007744|PDB:4M45
source Swiss-Prot : SWS_FT_FI6

26) chain A
residue 623
type BINDING
sequence D
description BINDING => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:15057283, ECO:0000269|PubMed:17718515, ECO:0000269|PubMed:20166748, ECO:0000269|PubMed:20166752, ECO:0000269|PubMed:21566148, ECO:0000269|PubMed:21923197, ECO:0000269|PubMed:22026756, ECO:0000305|PubMed:11389835, ECO:0000305|PubMed:15057282, ECO:0000305|PubMed:18503083, ECO:0000305|PubMed:21158418, ECO:0000305|PubMed:22571765, ECO:0000305|PubMed:23214497, ECO:0000305|PubMed:23921641, ECO:0000305|PubMed:24116139, ECO:0007744|PDB:2OZM, ECO:0007744|PDB:2OZS, ECO:0007744|PDB:3KD5, ECO:0007744|PDB:3SI6, ECO:0007744|PDB:3SNN, ECO:0007744|PDB:3SPY
source Swiss-Prot : SWS_FT_FI7


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