SMTL ID : 8rev.1

Structure of XPD stalled at a Y-fork DNA containing a interstrand crosslink

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 9 residues within 4Å: Chain A: R.111, C.115, L.116, H.117, C.133, C.154, H.157, C.189, F.192 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.115, A:C.133, A:C.154, A:C.189

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 13 residues within 4Å: Chain A: Y.14, R.16, I.17, Y.18, Q.21, G.45, T.46, G.47, K.48, T.49, I.50, E.85, E.234 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.14, A:Y.18, A:Q.21, A:Q.21, A:G.45, A:G.47, A:K.48, A:T.49, A:E.234 Salt bridges: A:K.81 pi-Stacking: A:Y.14, A:Y.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuper, J. et al., XPD stalled on cross-linked DNA provides insight into damage verification. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-05-29

Peptides

ATP-dependent DNA helicase CHL1: A
General transcription and DNA repair factor IIH: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

ATP-dependent DNA helicase CHL1

General transcription and DNA repair factor IIH