|
|
eF-site ID
|
3ndk-A |
|
PDB Code
|
3ndk |
|
Chain
|
A |
|
click to enlarge
|
|
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Title
|
RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite dG |
|
Classification
|
TRANSFERASE/DNA |
|
Compound
|
DNA polymerase |
|
Source
|
null (3NDK) |
|
|
Sequence
|
A: |
MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAH
CPESQATKYFDIYGKPCTRKLFANMRDASQWIKRMEDIGL
EALGMDDFKLAYLSDTYNYEIKYDHTKIRVANFDIEVTSP
DGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVE
EWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLME
YLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAK
RLSPHRKTRVKVIENMYGSREIITLFGISVLDYIDLYKKF
SFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRY
ISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFS
PIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPI
PNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLH
DYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFN
QRKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRF
DFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRK
LLINSLAGALGNVWFRYYDLRNATAITTFGQMALQWIERK
VNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESK
FRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHL
MFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRY
AEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESL
QEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPK
CPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNP
FGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPL
EGFTSAAKLDYEKKASLFDMFDF
|
|
|
Description
|
|
Functional site
|
|
|
1)
|
chain |
A |
| residue |
411 |
| type |
|
| sequence |
D
|
| description |
BINDING SITE FOR RESIDUE DCP A 904
|
| source |
: AC1
|
|
|
2)
|
chain |
A |
| residue |
412 |
| type |
|
| sequence |
L
|
| description |
BINDING SITE FOR RESIDUE DCP A 904
|
| source |
: AC1
|
|
|
3)
|
chain |
A |
| residue |
414 |
| type |
|
| sequence |
S
|
| description |
BINDING SITE FOR RESIDUE DCP A 904
|
| source |
: AC1
|
|
|
4)
|
chain |
A |
| residue |
415 |
| type |
|
| sequence |
L
|
| description |
BINDING SITE FOR RESIDUE DCP A 904
|
| source |
: AC1
|
|
|
5)
|
chain |
A |
| residue |
416 |
| type |
|
| sequence |
Y
|
| description |
BINDING SITE FOR RESIDUE DCP A 904
|
| source |
: AC1
|
|
|
6)
|
chain |
A |
| residue |
482 |
| type |
|
| sequence |
R
|
| description |
BINDING SITE FOR RESIDUE DCP A 904
|
| source |
: AC1
|
|
|
7)
|
chain |
A |
| residue |
560 |
| type |
|
| sequence |
K
|
| description |
BINDING SITE FOR RESIDUE DCP A 904
|
| source |
: AC1
|
|
|
8)
|
chain |
A |
| residue |
564 |
| type |
|
| sequence |
N
|
| description |
BINDING SITE FOR RESIDUE DCP A 904
|
| source |
: AC1
|
|
|
9)
|
chain |
A |
| residue |
622 |
| type |
|
| sequence |
T
|
| description |
BINDING SITE FOR RESIDUE DCP A 904
|
| source |
: AC1
|
|
|
10)
|
chain |
A |
| residue |
623 |
| type |
|
| sequence |
D
|
| description |
BINDING SITE FOR RESIDUE DCP A 904
|
| source |
: AC1
|
|
|
11)
|
chain |
A |
| residue |
411 |
| type |
|
| sequence |
D
|
| description |
BINDING SITE FOR RESIDUE CA A 905
|
| source |
: AC2
|
|
|
12)
|
chain |
A |
| residue |
412 |
| type |
|
| sequence |
L
|
| description |
BINDING SITE FOR RESIDUE CA A 905
|
| source |
: AC2
|
|
|
13)
|
chain |
A |
| residue |
623 |
| type |
|
| sequence |
D
|
| description |
BINDING SITE FOR RESIDUE CA A 905
|
| source |
: AC2
|
|
|
14)
|
chain |
A |
| residue |
411 |
| type |
|
| sequence |
D
|
| description |
BINDING SITE FOR RESIDUE CA A 906
|
| source |
: AC3
|
|
|
15)
|
chain |
A |
| residue |
623 |
| type |
|
| sequence |
D
|
| description |
BINDING SITE FOR RESIDUE CA A 906
|
| source |
: AC3
|
|
|
16)
|
chain |
A |
| residue |
505 |
| type |
|
| sequence |
N
|
| description |
BINDING SITE FOR RESIDUE CA A 907
|
| source |
: AC4
|
|
|
17)
|
chain |
A |
| residue |
507 |
| type |
|
| sequence |
N
|
| description |
BINDING SITE FOR RESIDUE CA A 907
|
| source |
: AC4
|
|
|
18)
|
chain |
A |
| residue |
531 |
| type |
|
| sequence |
K
|
| description |
BINDING SITE FOR RESIDUE CA A 907
|
| source |
: AC4
|
|
|
19)
|
chain |
A |
| residue |
411 |
| type |
|
| sequence |
D
|
| description |
BINDING SITE FOR RESIDUE CA A 908
|
| source |
: AC5
|
|
|
20)
|
chain |
A |
| residue |
686 |
| type |
|
| sequence |
E
|
| description |
BINDING SITE FOR RESIDUE CA A 908
|
| source |
: AC5
|
|
|
21)
|
chain |
A |
| residue |
716 |
| type |
|
| sequence |
E
|
| description |
BINDING SITE FOR RESIDUE CA A 908
|
| source |
: AC5
|
|
|
22)
|
chain |
A |
| residue |
116 |
| type |
|
| sequence |
E
|
| description |
BINDING SITE FOR RESIDUE CA A 909
|
| source |
: AC6
|
|
|
23)
|
chain |
A |
| residue |
612 |
| type |
|
| sequence |
E
|
| description |
BINDING SITE FOR RESIDUE CA A 910
|
| source |
: AC7
|
|
|
24)
|
chain |
A |
| residue |
792 |
| type |
|
| sequence |
D
|
| description |
BINDING SITE FOR RESIDUE CA A 910
|
| source |
: AC7
|
|
|
25)
|
chain |
A |
| residue |
144 |
| type |
|
| sequence |
D
|
| description |
BINDING SITE FOR RESIDUE CA A 911
|
| source |
: AC8
|
|
|
26)
|
chain |
A |
| residue |
185 |
| type |
|
| sequence |
K
|
| description |
BINDING SITE FOR RESIDUE CA A 911
|
| source |
: AC8
|
|
|
27)
|
chain |
A |
| residue |
114 |
| type |
BINDING |
| sequence |
D
|
| description |
BINDING => ECO:0000255|HAMAP-Rule:MF_04100
|
| source |
Swiss-Prot : SWS_FT_FI1
|
|
|
28)
|
chain |
A |
| residue |
116 |
| type |
BINDING |
| sequence |
E
|
| description |
BINDING => ECO:0000255|HAMAP-Rule:MF_04100
|
| source |
Swiss-Prot : SWS_FT_FI1
|
|
|
29)
|
chain |
A |
| residue |
222 |
| type |
BINDING |
| sequence |
A
|
| description |
BINDING => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000305|PubMed:23214497
|
| source |
Swiss-Prot : SWS_FT_FI2
|
|
|
30)
|
chain |
A |
| residue |
327 |
| type |
BINDING |
| sequence |
A
|
| description |
BINDING => ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000305|PubMed:23214497
|
| source |
Swiss-Prot : SWS_FT_FI2
|
|
|
31)
|
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
|
|
|
32)
|
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
|
|
|
33)
|
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
|
|
|
34)
|
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
|
|
|
35)
|
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
|
|
|
36)
|
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
|
|
|
37)
|
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
|
|
|
38)
|
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
|
|
|
39)
|
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
|
|
|
40)
|
chain |
A |
| residue |
619-627 |
| type |
prosite |
| sequence |
YGDTDSIYV
|
| description |
DNA_POLYMERASE_B DNA polymerase family B signature. YGDTDSIYV
|
| source |
prosite : PS00116
|
|
|
|