SMTL ID : 8ebv.1

Initial DNA-lesion (AP) binding by XPC and TFIIH complex 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-mer

Ligands

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 11 residues within 4Å: Chain B: R.112, C.116, I.117, H.118, V.121, C.134, T.138, C.155, F.157, C.190, F.193 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.116, B:C.134, B:C.155, B:C.190

5 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain E: C.367, C.370, C.390, C.393 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.367, E:C.370, E:C.390, E:C.393 ZN.3: 4 residues within 4Å: Chain E: C.382, C.385, C.404, C.407 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.382, E:C.385, E:C.404, E:C.407 ZN.4: 4 residues within 4Å: Chain E: C.313, C.316, C.327, C.330 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.313, E:C.316, E:C.327, E:C.330 ZN.5: 5 residues within 4Å: Chain F: C.268, C.271, S.273, C.282, C.285 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.268, F:C.271, F:C.282, F:C.285 ZN.6: 4 residues within 4Å: Chain F: C.255, C.257, H.258, C.276 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.255, F:C.257, F:H.258, F:C.276

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 6 residues within 4Å: Chain J: D.114, D.116, T.118, K.120, S.122, N.125 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:D.116, J:D.116, J:T.118 CA.8: 6 residues within 4Å: Chain J: D.152, D.154, E.156, V.157, S.158, E.161 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.154, J:E.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, J. et al., Lesion recognition by XPC, TFIIH and XPA in DNA excision repair. Nature (2023)

Release Date

2023-04-19

Peptides

TFIIH basal transcription factor complex helicase XPB subunit: A
General transcription and DNA repair factor IIH helicase subunit XPD: B
General transcription factor IIH subunit 1: C
General transcription factor IIH subunit 4, p52: D
General transcription factor IIH subunit 2: E
General transcription factor IIH subunit 3: F
General transcription factor IIH subunit 5: G
DNA repair protein complementing XP-C cells: H
UV excision repair protein RAD23 homolog B: I
Centrin-2: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

TFIIH basal transcription factor complex helicase XPB subunit

General transcription and DNA repair factor IIH helicase subunit XPD

General transcription factor IIH subunit 1

General transcription factor IIH subunit 4, p52

General transcription factor IIH subunit 2

General transcription factor IIH subunit 3

General transcription factor IIH subunit 5

DNA repair protein complementing XP-C cells

UV excision repair protein RAD23 homolog B

Centrin-2

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