eF-site ID 5dkw-AB
PDB Code 5dkw
Chain A, B

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Title Ternary crystal structure of polymerase lambda with a GA mispair at the primer terminus with Ca2+ in the active
Classification TRANSFERASE/DNA
Compound DNA polymerase lambda
Source (5DKW)
Sequence A:  ATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKS
FHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHI
SESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQAS
LTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNS
GLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLL
DSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRR
LDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLS
EHALSTAVVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
B:  ATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKS
FHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHI
SESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQAS
LTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNS
GLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLL
DSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRR
LDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLS
EHALSTAVVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Description


Functional site

1) chain A
residue 386
type
sequence R
description binding site for residue DTP A 601
source : AC1

2) chain A
residue 416
type
sequence G
description binding site for residue DTP A 601
source : AC1

3) chain A
residue 417
type
sequence S
description binding site for residue DTP A 601
source : AC1

4) chain A
residue 420
type
sequence R
description binding site for residue DTP A 601
source : AC1

5) chain A
residue 426
type
sequence G
description binding site for residue DTP A 601
source : AC1

6) chain A
residue 427
type
sequence D
description binding site for residue DTP A 601
source : AC1

7) chain A
residue 429
type
sequence D
description binding site for residue DTP A 601
source : AC1

8) chain A
residue 505
type
sequence Y
description binding site for residue DTP A 601
source : AC1

9) chain A
residue 506
type
sequence F
description binding site for residue DTP A 601
source : AC1

10) chain A
residue 508
type
sequence G
description binding site for residue DTP A 601
source : AC1

11) chain A
residue 513
type
sequence N
description binding site for residue DTP A 601
source : AC1

12) chain A
residue 427
type
sequence D
description binding site for residue CA A 602
source : AC2

13) chain A
residue 300
type
sequence C
description binding site for residue CA A 603
source : AC3

14) chain A
residue 302
type
sequence I
description binding site for residue CA A 603
source : AC3

15) chain A
residue 305
type
sequence I
description binding site for residue CA A 603
source : AC3

16) chain B
residue 300
type
sequence C
description binding site for residue CA B 601
source : AC4

17) chain B
residue 302
type
sequence I
description binding site for residue CA B 601
source : AC4

18) chain B
residue 305
type
sequence I
description binding site for residue CA B 601
source : AC4

19) chain B
residue 339
type
sequence S
description binding site for residue CA B 602
source : AC5

20) chain B
residue 341
type
sequence I
description binding site for residue CA B 602
source : AC5

21) chain B
residue 344
type
sequence A
description binding site for residue CA B 602
source : AC5

22) chain B
residue 386
type
sequence R
description binding site for residue DTP B 603
source : AC6

23) chain B
residue 416
type
sequence G
description binding site for residue DTP B 603
source : AC6

24) chain B
residue 417
type
sequence S
description binding site for residue DTP B 603
source : AC6

25) chain B
residue 420
type
sequence R
description binding site for residue DTP B 603
source : AC6

26) chain B
residue 426
type
sequence G
description binding site for residue DTP B 603
source : AC6

27) chain B
residue 427
type
sequence D
description binding site for residue DTP B 603
source : AC6

28) chain B
residue 429
type
sequence D
description binding site for residue DTP B 603
source : AC6

29) chain B
residue 505
type
sequence Y
description binding site for residue DTP B 603
source : AC6

30) chain B
residue 506
type
sequence F
description binding site for residue DTP B 603
source : AC6

31) chain B
residue 508
type
sequence G
description binding site for residue DTP B 603
source : AC6

32) chain B
residue 513
type
sequence N
description binding site for residue DTP B 603
source : AC6

33) chain B
residue 427
type
sequence D
description binding site for residue CA B 604
source : AC7

34) chain B
residue 429
type
sequence D
description binding site for residue CA B 604
source : AC7

35) chain A
residue 416-435
type prosite
sequence GSYRRGKATCGDVDVLITHP
description DNA_POLYMERASE_X DNA polymerase family X signature. GSYrRGkatCgDVDVLIthP
source prosite : PS00522

36) chain A
residue 312
type ACT_SITE
sequence K
description Schiff-base intermediate with DNA => ECO:0000269|PubMed:11457865
source Swiss-Prot : SWS_FT_FI1

37) chain B
residue 312
type ACT_SITE
sequence K
description Schiff-base intermediate with DNA => ECO:0000269|PubMed:11457865
source Swiss-Prot : SWS_FT_FI1

38) chain A
residue 386
type BINDING
sequence R
description BINDING => ECO:0000269|PubMed:17475573, ECO:0007744|PDB:2PFP, ECO:0007744|PDB:2PFQ
source Swiss-Prot : SWS_FT_FI2

39) chain A
residue 417
type BINDING
sequence S
description BINDING => ECO:0000269|PubMed:17475573, ECO:0007744|PDB:2PFP, ECO:0007744|PDB:2PFQ
source Swiss-Prot : SWS_FT_FI2

40) chain A
residue 426
type BINDING
sequence G
description BINDING => ECO:0000269|PubMed:17475573, ECO:0007744|PDB:2PFP, ECO:0007744|PDB:2PFQ
source Swiss-Prot : SWS_FT_FI2

41) chain A
residue 513
type BINDING
sequence N
description BINDING => ECO:0000269|PubMed:17475573, ECO:0007744|PDB:2PFP, ECO:0007744|PDB:2PFQ
source Swiss-Prot : SWS_FT_FI2

42) chain B
residue 386
type BINDING
sequence R
description BINDING => ECO:0000269|PubMed:17475573, ECO:0007744|PDB:2PFP, ECO:0007744|PDB:2PFQ
source Swiss-Prot : SWS_FT_FI2

43) chain B
residue 417
type BINDING
sequence S
description BINDING => ECO:0000269|PubMed:17475573, ECO:0007744|PDB:2PFP, ECO:0007744|PDB:2PFQ
source Swiss-Prot : SWS_FT_FI2

44) chain B
residue 426
type BINDING
sequence G
description BINDING => ECO:0000269|PubMed:17475573, ECO:0007744|PDB:2PFP, ECO:0007744|PDB:2PFQ
source Swiss-Prot : SWS_FT_FI2

45) chain B
residue 513
type BINDING
sequence N
description BINDING => ECO:0000269|PubMed:17475573, ECO:0007744|PDB:2PFP, ECO:0007744|PDB:2PFQ
source Swiss-Prot : SWS_FT_FI2

46) chain A
residue 427
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:17475573, ECO:0007744|PDB:2PFO, ECO:0007744|PDB:2PFQ
source Swiss-Prot : SWS_FT_FI3

47) chain A
residue 429
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:17475573, ECO:0007744|PDB:2PFO, ECO:0007744|PDB:2PFQ
source Swiss-Prot : SWS_FT_FI3

48) chain A
residue 490
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:17475573, ECO:0007744|PDB:2PFO, ECO:0007744|PDB:2PFQ
source Swiss-Prot : SWS_FT_FI3

49) chain B
residue 427
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:17475573, ECO:0007744|PDB:2PFO, ECO:0007744|PDB:2PFQ
source Swiss-Prot : SWS_FT_FI3

50) chain B
residue 429
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:17475573, ECO:0007744|PDB:2PFO, ECO:0007744|PDB:2PFQ
source Swiss-Prot : SWS_FT_FI3

51) chain B
residue 490
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:17475573, ECO:0007744|PDB:2PFO, ECO:0007744|PDB:2PFQ
source Swiss-Prot : SWS_FT_FI3


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