eF-site ID 9icw-A
PDB Code 9icw
Chain A

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Title DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; NATIVE STRUCTURE
Classification TRANSFERASE/DNA
Compound DNA (5'-D(*CP*AP*TP*CP*TP*GP*T)-3')
Source Homo sapiens (Human) (9ICW)
Sequence A:  ETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAK
YPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKI
RQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKN
EDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKK
VDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQP
KLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEK
EYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALE
KGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYR
EPKDRSE
Description


Functional site

1) chain A
residue 149
type
sequence R
description BINDING SITE FOR RESIDUE SO4 A 338
source : AC1

2) chain A
residue 180
type
sequence S
description BINDING SITE FOR RESIDUE SO4 A 338
source : AC1

3) chain A
residue 189
type
sequence G
description BINDING SITE FOR RESIDUE SO4 A 338
source : AC1

4) chain A
residue 101
type
sequence T
description BINDING SITE FOR RESIDUE NA A 341
source : AC2

5) chain A
residue 103
type
sequence V
description BINDING SITE FOR RESIDUE NA A 341
source : AC2

6) chain A
residue 106
type
sequence I
description BINDING SITE FOR RESIDUE NA A 341
source : AC2

7) chain A
residue 60
type
sequence K
description BINDING SITE FOR RESIDUE NA A 342
source : AC3

8) chain A
residue 62
type
sequence L
description BINDING SITE FOR RESIDUE NA A 342
source : AC3

9) chain A
residue 65
type
sequence V
description BINDING SITE FOR RESIDUE NA A 342
source : AC3

10) chain A
residue 150
type BINDING
sequence I
description BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICW, ECO:0007744|PDB:8ICX, ECO:0007744|PDB:8ICY
source Swiss-Prot : SWS_FT_FI3

11) chain A
residue 181
type BINDING
sequence F
description BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICW, ECO:0007744|PDB:8ICX, ECO:0007744|PDB:8ICY
source Swiss-Prot : SWS_FT_FI3

12) chain A
residue 190
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICW, ECO:0007744|PDB:8ICX, ECO:0007744|PDB:8ICY
source Swiss-Prot : SWS_FT_FI3

13) chain A
residue 179-198
type prosite
sequence GSFRRGAESSGDMDVLLTHP
description DNA_POLYMERASE_X DNA polymerase family X signature. GSFrRGaesSgDMDVLLthP
source prosite : PS00522

14) chain A
residue 73
type MOD_RES
sequence I
description N6-acetyllysine => ECO:0000250|UniProtKB:Q8K409
source Swiss-Prot : SWS_FT_FI6

15) chain A
residue 84
type MOD_RES
sequence K
description Omega-N-methylarginine; by PRMT6 => ECO:0000269|PubMed:16600869
source Swiss-Prot : SWS_FT_FI7

16) chain A
residue 153
type MOD_RES
sequence E
description Omega-N-methylarginine; by PRMT6 => ECO:0000269|PubMed:16600869
source Swiss-Prot : SWS_FT_FI7

17) chain A
residue 42
type CROSSLNK
sequence A
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:19713937, ECO:0000269|PubMed:21362556
source Swiss-Prot : SWS_FT_FI8

18) chain A
residue 62
type CROSSLNK
sequence L
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:19713937, ECO:0000269|PubMed:21362556
source Swiss-Prot : SWS_FT_FI8

19) chain A
residue 82
type CROSSLNK
sequence L
description Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:19713937, ECO:0000269|PubMed:21362556
source Swiss-Prot : SWS_FT_FI8

20) chain A
residue 73
type ACT_SITE
sequence I
description Nucleophile; Schiff-base intermediate with DNA; for 5'-dRP lyase activity => ECO:0000269|PubMed:9572863
source Swiss-Prot : SWS_FT_FI1

21) chain A
residue 61
type BINDING
sequence K
description BINDING => ECO:0000269|PubMed:12517346, ECO:0000269|PubMed:8841120, ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPX, ECO:0007744|PDB:1BPZ, ECO:0007744|PDB:1MQ3, ECO:0007744|PDB:1ZQO, ECO:0007744|PDB:1ZQQ
source Swiss-Prot : SWS_FT_FI2

22) chain A
residue 63
type BINDING
sequence P
description BINDING => ECO:0000269|PubMed:12517346, ECO:0000269|PubMed:8841120, ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPX, ECO:0007744|PDB:1BPZ, ECO:0007744|PDB:1MQ3, ECO:0007744|PDB:1ZQO, ECO:0007744|PDB:1ZQQ
source Swiss-Prot : SWS_FT_FI2

23) chain A
residue 66
type BINDING
sequence G
description BINDING => ECO:0000269|PubMed:12517346, ECO:0000269|PubMed:8841120, ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPX, ECO:0007744|PDB:1BPZ, ECO:0007744|PDB:1MQ3, ECO:0007744|PDB:1ZQO, ECO:0007744|PDB:1ZQQ
source Swiss-Prot : SWS_FT_FI2

24) chain A
residue 102
type BINDING
sequence R
description BINDING => ECO:0000269|PubMed:12517346, ECO:0000269|PubMed:8841120, ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPX, ECO:0007744|PDB:1BPZ, ECO:0007744|PDB:1MQ3, ECO:0007744|PDB:1ZQO, ECO:0007744|PDB:1ZQQ
source Swiss-Prot : SWS_FT_FI2

25) chain A
residue 104
type BINDING
sequence S
description BINDING => ECO:0000269|PubMed:12517346, ECO:0000269|PubMed:8841120, ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPX, ECO:0007744|PDB:1BPZ, ECO:0007744|PDB:1MQ3, ECO:0007744|PDB:1ZQO, ECO:0007744|PDB:1ZQQ
source Swiss-Prot : SWS_FT_FI2

26) chain A
residue 107
type BINDING
sequence G
description BINDING => ECO:0000269|PubMed:12517346, ECO:0000269|PubMed:8841120, ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPX, ECO:0007744|PDB:1BPZ, ECO:0007744|PDB:1MQ3, ECO:0007744|PDB:1ZQO, ECO:0007744|PDB:1ZQQ
source Swiss-Prot : SWS_FT_FI2

27) chain A
residue 184
type BINDING
sequence G
description BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICX
source Swiss-Prot : SWS_FT_FI4

28) chain A
residue 191
type BINDING
sequence M
description BINDING => ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPY
source Swiss-Prot : SWS_FT_FI5

29) chain A
residue 193
type BINDING
sequence V
description BINDING => ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPY
source Swiss-Prot : SWS_FT_FI5

30) chain A
residue 257
type BINDING
sequence I
description BINDING => ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPY
source Swiss-Prot : SWS_FT_FI5


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