eF-site ID 1e9n-AB
PDB Code 1e9n
Chain A, B

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Title A second divalent metal ion in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1, and its implications for the catalytic mechanism
Classification DNA REPAIR
Compound DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE
Source (APE1_HUMAN)
Sequence A:  ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLD
WVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAP
SEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDS
FVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKP
LVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELL
QAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDY
FLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
B:  ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLD
WVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAP
SEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDS
FVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKP
LVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELL
QAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDY
FLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
Description


Functional site

1) chain A
residue 70
type
sequence D
description BINDING SITE FOR RESIDUE PB A1319
source : AC1

2) chain A
residue 96
type
sequence E
description BINDING SITE FOR RESIDUE PB A1319
source : AC1

3) chain A
residue 210
type
sequence D
description BINDING SITE FOR RESIDUE PB A1320
source : AC2

4) chain A
residue 212
type
sequence N
description BINDING SITE FOR RESIDUE PB A1320
source : AC2

5) chain A
residue 309
type
sequence H
description BINDING SITE FOR RESIDUE PB A1320
source : AC2

6) chain B
residue 210
type
sequence D
description BINDING SITE FOR RESIDUE PB B1319
source : AC3

7) chain B
residue 212
type
sequence N
description BINDING SITE FOR RESIDUE PB B1319
source : AC3

8) chain B
residue 282
type
sequence L
description BINDING SITE FOR RESIDUE PB B1319
source : AC3

9) chain B
residue 309
type
sequence H
description BINDING SITE FOR RESIDUE PB B1319
source : AC3

10) chain B
residue 96
type
sequence E
description BINDING SITE FOR RESIDUE PB B1320
source : AC4

11) chain A
residue 71
type catalytic
sequence G
description 510
source MCSA : MCSA1

12) chain A
residue 97
type catalytic
sequence T
description 510
source MCSA : MCSA1

13) chain A
residue 172
type catalytic
sequence V
description 510
source MCSA : MCSA1

14) chain A
residue 211
type catalytic
sequence L
description 510
source MCSA : MCSA1

15) chain A
residue 213
type catalytic
sequence V
description 510
source MCSA : MCSA1

16) chain A
residue 284
type catalytic
sequence Y
description 510
source MCSA : MCSA1

17) chain A
residue 309
type catalytic
sequence H
description 510
source MCSA : MCSA1

18) chain A
residue 310
type catalytic
sequence C
description 510
source MCSA : MCSA1

19) chain B
residue 71
type catalytic
sequence G
description 510
source MCSA : MCSA2

20) chain B
residue 97
type catalytic
sequence T
description 510
source MCSA : MCSA2

21) chain B
residue 172
type catalytic
sequence V
description 510
source MCSA : MCSA2

22) chain B
residue 211
type catalytic
sequence L
description 510
source MCSA : MCSA2

23) chain B
residue 213
type catalytic
sequence V
description 510
source MCSA : MCSA2

24) chain B
residue 284
type catalytic
sequence Y
description 510
source MCSA : MCSA2

25) chain B
residue 309
type catalytic
sequence H
description 510
source MCSA : MCSA2

26) chain B
residue 310
type catalytic
sequence C
description 510
source MCSA : MCSA2

27) chain A
residue 89-98
type prosite
sequence PDILCLQETK
description AP_NUCLEASE_F1_1 AP endonucleases family 1 signature 1. PDILCLQETK
source prosite : PS00726

28) chain A
residue 251-267
type prosite
sequence DSFRHLYPNTPYAYTFW
description AP_NUCLEASE_F1_2 AP endonucleases family 1 signature 2. DSFRHlypntpyaYTFW
source prosite : PS00727

29) chain A
residue 277-288
type prosite
sequence NVGWRLDYFLLS
description AP_NUCLEASE_F1_3 AP endonucleases family 1 signature 3. NvGwRLDYfLlS
source prosite : PS00728

30) chain A
residue 172
type ACT_SITE
sequence V
description ACT_SITE => ECO:0000269|PubMed:15380100
source Swiss-Prot : SWS_FT_FI1

31) chain B
residue 172
type ACT_SITE
sequence V
description ACT_SITE => ECO:0000269|PubMed:15380100
source Swiss-Prot : SWS_FT_FI1

32) chain A
residue 55
type MOD_RES
sequence P
description Phosphoserine => ECO:0007744|PubMed:23186163
source Swiss-Prot : SWS_FT_FI11

33) chain B
residue 55
type MOD_RES
sequence P
description Phosphoserine => ECO:0007744|PubMed:23186163
source Swiss-Prot : SWS_FT_FI11

34) chain A
residue 66
type MOD_RES
sequence S
description S-nitrosocysteine; alternate => ECO:0000269|PubMed:17403694
source Swiss-Prot : SWS_FT_FI12

35) chain A
residue 94
type MOD_RES
sequence L
description S-nitrosocysteine; alternate => ECO:0000269|PubMed:17403694
source Swiss-Prot : SWS_FT_FI12

36) chain B
residue 66
type MOD_RES
sequence S
description S-nitrosocysteine; alternate => ECO:0000269|PubMed:17403694
source Swiss-Prot : SWS_FT_FI12

37) chain B
residue 94
type MOD_RES
sequence L
description S-nitrosocysteine; alternate => ECO:0000269|PubMed:17403694
source Swiss-Prot : SWS_FT_FI12

38) chain A
residue 198
type MOD_RES
sequence G
description N6-acetyllysine => ECO:0007744|PubMed:19608861
source Swiss-Prot : SWS_FT_FI13

39) chain B
residue 198
type MOD_RES
sequence G
description N6-acetyllysine => ECO:0007744|PubMed:19608861
source Swiss-Prot : SWS_FT_FI13

40) chain A
residue 234
type MOD_RES
sequence P
description Phosphothreonine; by CDK5 => ECO:0000250|UniProtKB:P28352
source Swiss-Prot : SWS_FT_FI14

41) chain B
residue 234
type MOD_RES
sequence P
description Phosphothreonine; by CDK5 => ECO:0000250|UniProtKB:P28352
source Swiss-Prot : SWS_FT_FI14

42) chain A
residue 311
type MOD_RES
sequence P
description S-nitrosocysteine => ECO:0000269|PubMed:17403694
source Swiss-Prot : SWS_FT_FI15

43) chain B
residue 311
type MOD_RES
sequence P
description S-nitrosocysteine => ECO:0000269|PubMed:17403694
source Swiss-Prot : SWS_FT_FI15

44) chain A
residue 211
type ACT_SITE
sequence L
description Proton donor/acceptor => ECO:0000269|PubMed:9351835, ECO:0007744|PDB:1BIX
source Swiss-Prot : SWS_FT_FI2

45) chain B
residue 211
type ACT_SITE
sequence L
description Proton donor/acceptor => ECO:0000269|PubMed:9351835, ECO:0007744|PDB:1BIX
source Swiss-Prot : SWS_FT_FI2

46) chain A
residue 310
type ACT_SITE
sequence C
description Proton acceptor => ECO:0000255|PROSITE-ProRule:PRU00764
source Swiss-Prot : SWS_FT_FI3

47) chain B
residue 310
type ACT_SITE
sequence C
description Proton acceptor => ECO:0000255|PROSITE-ProRule:PRU00764
source Swiss-Prot : SWS_FT_FI3

48) chain A
residue 69
type BINDING
sequence V
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764
source Swiss-Prot : SWS_FT_FI4

49) chain B
residue 213
type BINDING
sequence V
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764
source Swiss-Prot : SWS_FT_FI4

50) chain B
residue 309
type BINDING
sequence H
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764
source Swiss-Prot : SWS_FT_FI4

51) chain B
residue 310
type BINDING
sequence C
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764
source Swiss-Prot : SWS_FT_FI4

52) chain A
residue 97
type BINDING
sequence T
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764
source Swiss-Prot : SWS_FT_FI4

53) chain A
residue 211
type BINDING
sequence L
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764
source Swiss-Prot : SWS_FT_FI4

54) chain A
residue 213
type BINDING
sequence V
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764
source Swiss-Prot : SWS_FT_FI4

55) chain A
residue 309
type BINDING
sequence H
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764
source Swiss-Prot : SWS_FT_FI4

56) chain A
residue 310
type BINDING
sequence C
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764
source Swiss-Prot : SWS_FT_FI4

57) chain B
residue 69
type BINDING
sequence V
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764
source Swiss-Prot : SWS_FT_FI4

58) chain B
residue 97
type BINDING
sequence T
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764
source Swiss-Prot : SWS_FT_FI4

59) chain B
residue 211
type BINDING
sequence L
description BINDING => ECO:0000255|PROSITE-ProRule:PRU00764
source Swiss-Prot : SWS_FT_FI4

60) chain A
residue 213
type SITE
sequence V
description Transition state stabilizer => ECO:0000269|PubMed:8932375
source Swiss-Prot : SWS_FT_FI6

61) chain B
residue 213
type SITE
sequence V
description Transition state stabilizer => ECO:0000269|PubMed:8932375
source Swiss-Prot : SWS_FT_FI6

62) chain A
residue 284
type SITE
sequence Y
description Important for catalytic activity => ECO:0000269|PubMed:21762700, ECO:0000269|PubMed:9804799
source Swiss-Prot : SWS_FT_FI7

63) chain B
residue 284
type SITE
sequence Y
description Important for catalytic activity => ECO:0000269|PubMed:21762700, ECO:0000269|PubMed:9804799
source Swiss-Prot : SWS_FT_FI7

64) chain A
residue 310
type SITE
sequence C
description Interaction with DNA substrate
source Swiss-Prot : SWS_FT_FI8

65) chain B
residue 310
type SITE
sequence C
description Interaction with DNA substrate
source Swiss-Prot : SWS_FT_FI8


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