eF-site ID 5j2b-ADPT
PDB Code 5j2b
Chain A, D, P, T

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Title Ternary complex crystal structure of DNA polymerase Beta with A:C mismatch at the primer terminus
Classification Transferase/DNA
Compound DNA polymerase beta
Source Homo sapiens (Human) (5J2B)
Sequence A:  TLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKY
PHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIR
QDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNE
DKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKV
DSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPK
LLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKE
YPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEK
GFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYRE
PKDRSE
D:  GTCGG
P:  GCTGATGCGG
T:  CCGACAACGCATCAGC
Description


Functional site

1) chain A
residue 179
type
sequence G
description binding site for residue DUP A 401
source : AC1

2) chain A
residue 180
type
sequence S
description binding site for residue DUP A 401
source : AC1

3) chain A
residue 183
type
sequence R
description binding site for residue DUP A 401
source : AC1

4) chain A
residue 189
type
sequence G
description binding site for residue DUP A 401
source : AC1

5) chain A
residue 190
type
sequence D
description binding site for residue DUP A 401
source : AC1

6) chain A
residue 192
type
sequence D
description binding site for residue DUP A 401
source : AC1

7) chain A
residue 271
type
sequence Y
description binding site for residue DUP A 401
source : AC1

8) chain A
residue 272
type
sequence F
description binding site for residue DUP A 401
source : AC1

9) chain A
residue 273
type
sequence T
description binding site for residue DUP A 401
source : AC1

10) chain A
residue 274
type
sequence G
description binding site for residue DUP A 401
source : AC1

11) chain A
residue 276
type
sequence D
description binding site for residue DUP A 401
source : AC1

12) chain A
residue 279
type
sequence N
description binding site for residue DUP A 401
source : AC1

13) chain P
residue 10
type
sequence G
description binding site for residue DUP A 401
source : AC1

14) chain T
residue 6
type
sequence A
description binding site for residue DUP A 401
source : AC1

15) chain A
residue 190
type
sequence D
description binding site for residue MG A 402
source : AC2

16) chain A
residue 192
type
sequence D
description binding site for residue MG A 402
source : AC2

17) chain A
residue 190
type
sequence D
description binding site for residue MG A 403
source : AC3

18) chain A
residue 192
type
sequence D
description binding site for residue MG A 403
source : AC3

19) chain A
residue 256
type
sequence D
description binding site for residue MG A 403
source : AC3

20) chain A
residue 101
type
sequence T
description binding site for residue NA A 404
source : AC4

21) chain A
residue 103
type
sequence V
description binding site for residue NA A 404
source : AC4

22) chain A
residue 106
type
sequence I
description binding site for residue NA A 404
source : AC4

23) chain P
residue 9
type
sequence G
description binding site for residue NA A 404
source : AC4

24) chain A
residue 60
type
sequence K
description binding site for residue NA A 405
source : AC5

25) chain A
residue 62
type
sequence L
description binding site for residue NA A 405
source : AC5

26) chain A
residue 65
type
sequence V
description binding site for residue NA A 405
source : AC5

27) chain D
residue 3
type
sequence C
description binding site for residue NA A 405
source : AC5

28) chain A
residue 294
type
sequence N
description binding site for residue CL A 406
source : AC6

29) chain A
residue 297
type
sequence T
description binding site for residue CL A 406
source : AC6

30) chain A
residue 299
type
sequence R
description binding site for residue CL A 406
source : AC6

31) chain A
residue 32
type
sequence A
description binding site for residue CL A 407
source : AC7

32) chain A
residue 34
type
sequence H
description binding site for residue CL A 407
source : AC7

33) chain A
residue 35
type
sequence K
description binding site for residue CL A 407
source : AC7

34) chain A
residue 72
type MOD_RES
sequence K
description N6-acetyllysine => ECO:0000250|UniProtKB:Q8K409
source Swiss-Prot : SWS_FT_FI6

35) chain A
residue 83
type MOD_RES
sequence R
description Omega-N-methylarginine; by PRMT6 => ECO:0000269|PubMed:16600869
source Swiss-Prot : SWS_FT_FI7

36) chain A
residue 152
type MOD_RES
sequence R
description Omega-N-methylarginine; by PRMT6 => ECO:0000269|PubMed:16600869
source Swiss-Prot : SWS_FT_FI7

37) chain A
residue 41
type CROSSLNK
sequence K
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

38) chain A
residue 61
type CROSSLNK
sequence K
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

39) chain A
residue 81
type CROSSLNK
sequence K
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

40) chain A
residue 72
type ACT_SITE
sequence K
description Nucleophile; Schiff-base intermediate with DNA; for 5'-dRP lyase activity => ECO:0000269|PubMed:9572863
source Swiss-Prot : SWS_FT_FI1

41) chain A
residue 60
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

42) chain A
residue 62
type BINDING
sequence L
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

43) chain A
residue 65
type BINDING
sequence V
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

44) chain A
residue 101
type BINDING
sequence T
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

45) chain A
residue 103
type BINDING
sequence V
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

46) chain A
residue 106
type BINDING
sequence I
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

47) chain A
residue 149
type BINDING
sequence R
description BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICW, ECO:0007744|PDB:8ICX, ECO:0007744|PDB:8ICY
source Swiss-Prot : SWS_FT_FI3

48) chain A
residue 180
type BINDING
sequence S
description BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICW, ECO:0007744|PDB:8ICX, ECO:0007744|PDB:8ICY
source Swiss-Prot : SWS_FT_FI3

49) chain A
residue 189
type BINDING
sequence G
description BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICW, ECO:0007744|PDB:8ICX, ECO:0007744|PDB:8ICY
source Swiss-Prot : SWS_FT_FI3

50) chain A
residue 183
type BINDING
sequence R
description BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICX
source Swiss-Prot : SWS_FT_FI4

51) chain A
residue 190
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPY
source Swiss-Prot : SWS_FT_FI5

52) chain A
residue 192
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPY
source Swiss-Prot : SWS_FT_FI5

53) chain A
residue 256
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPY
source Swiss-Prot : SWS_FT_FI5

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


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