eF-site ID 5wny-A
PDB Code 5wny
Chain A

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Title DNA polymerase beta substrate complex with incoming 5-FdUTP
Classification DNA LIGASE/DNA, TRANSFERASE
Compound DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Source (DPOLB_HUMAN)
Sequence A:  TLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKY
PHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIR
QDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNE
DKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKV
DSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPK
LLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKE
YPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEK
GFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYRE
PKDRSE
Description


Functional site
1) chain A
residue 101
type
sequence T
description binding site for residue NA A 401
source : AC1
2) chain A
residue 103
type
sequence V
description binding site for residue NA A 401
source : AC1
3) chain A
residue 106
type
sequence I
description binding site for residue NA A 401
source : AC1
4) chain A
residue 60
type
sequence K
description binding site for residue NA A 402
source : AC2
5) chain A
residue 62
type
sequence L
description binding site for residue NA A 402
source : AC2
6) chain A
residue 65
type
sequence V
description binding site for residue NA A 402
source : AC2
7) chain A
residue 263
type
sequence D
description binding site for residue CL A 403
source : AC3
8) chain A
residue 264
type
sequence Q
description binding site for residue CL A 403
source : AC3
9) chain A
residue 266
type
sequence Y
description binding site for residue CL A 403
source : AC3
10) chain A
residue 267
type
sequence C
description binding site for residue CL A 403
source : AC3
11) chain A
residue 313
type
sequence V
description binding site for residue CL A 403
source : AC3
12) chain A
residue 32
type
sequence A
description binding site for residue CL A 404
source : AC4
13) chain A
residue 33
type
sequence I
description binding site for residue CL A 404
source : AC4
14) chain A
residue 34
type
sequence H
description binding site for residue CL A 404
source : AC4
15) chain A
residue 81
type
sequence K
description binding site for residue CL A 405
source : AC5
16) chain A
residue 82
type
sequence L
description binding site for residue CL A 405
source : AC5
17) chain A
residue 294
type
sequence N
description binding site for residue CL A 406
source : AC6
18) chain A
residue 297
type
sequence T
description binding site for residue CL A 406
source : AC6
19) chain A
residue 299
type
sequence R
description binding site for residue CL A 406
source : AC6
20) chain A
residue 190
type
sequence D
description binding site for residue CA A 407
source : AC7
21) chain A
residue 192
type
sequence D
description binding site for residue CA A 407
source : AC7
22) chain A
residue 190
type
sequence D
description binding site for residue CA A 408
source : AC8
23) chain A
residue 192
type
sequence D
description binding site for residue CA A 408
source : AC8
24) chain A
residue 256
type
sequence D
description binding site for residue CA A 408
source : AC8
25) chain A
residue 149
type
sequence R
description binding site for residue B7P A 409
source : AC9
26) chain A
residue 179
type
sequence G
description binding site for residue B7P A 409
source : AC9
27) chain A
residue 180
type
sequence S
description binding site for residue B7P A 409
source : AC9
28) chain A
residue 183
type
sequence R
description binding site for residue B7P A 409
source : AC9
29) chain A
residue 188
type
sequence S
description binding site for residue B7P A 409
source : AC9
30) chain A
residue 189
type
sequence G
description binding site for residue B7P A 409
source : AC9
31) chain A
residue 190
type
sequence D
description binding site for residue B7P A 409
source : AC9
32) chain A
residue 192
type
sequence D
description binding site for residue B7P A 409
source : AC9
33) chain A
residue 271
type
sequence Y
description binding site for residue B7P A 409
source : AC9
34) chain A
residue 272
type
sequence F
description binding site for residue B7P A 409
source : AC9
35) chain A
residue 273
type
sequence T
description binding site for residue B7P A 409
source : AC9
36) chain A
residue 274
type
sequence G
description binding site for residue B7P A 409
source : AC9
37) chain A
residue 276
type
sequence D
description binding site for residue B7P A 409
source : AC9
38) chain A
residue 279
type
sequence N
description binding site for residue B7P A 409
source : AC9
39) chain A
residue 179-198
type prosite
sequence GSFRRGAESSGDMDVLLTHP
description DNA_POLYMERASE_X DNA polymerase family X signature. GSFrRGaesSgDMDVLLthP
source prosite : PS00522
40) chain A
residue 72
type MOD_RES
sequence K
description N6-acetyllysine => ECO:0000250|UniProtKB:Q8K409
source Swiss-Prot : SWS_FT_FI6
41) 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
42) 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
43) 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
44) 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
45) 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
46) 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
47) 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
48) 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
49) 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
50) 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
51) 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
52) 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
53) 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
54) 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
55) 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
56) chain A
residue 183
type BINDING
sequence R
description BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICX
source Swiss-Prot : SWS_FT_FI4
57) chain A
residue 190
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPY
source Swiss-Prot : SWS_FT_FI5
58) chain A
residue 192
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPY
source Swiss-Prot : SWS_FT_FI5
59) chain A
residue 256
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPY
source Swiss-Prot : SWS_FT_FI5

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