SMTL ID : 3m9n.1

Crystal Structure of Dpo4 in complex with DNA containing the major cisplatin lesion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: D.7, E.106 Chain B: C.13 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.7, A:E.106, H2O.1, H2O.3, H2O.3 CA.2: 2 residues within 4Å: Chain A: A.181, I.186 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.181, A:I.186, H2O.1, H2O.10, H2O.10 CA.3: 4 residues within 4Å: Chain A: D.7, F.8, D.105 Ligands: CTP.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.7, A:F.8, A:D.105

1 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.4: 16 residues within 4Å: Chain A: D.7, F.8, D.9, Y.10, F.11, Y.12, A.44, T.45, R.51, A.57, M.76, D.105, K.159 Chain B: C.13 Chain C: G.4 Ligands: CA.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.12, A:T.45, A:A.57 Hydrogen bonds: A:Y.10, A:F.11, A:Y.12, A:T.45 Water bridges: A:R.51 Salt bridges: A:R.51, A:R.51, A:K.159

1 x CPT: Cisplatin(Non-functional Binders)

CPT.5: 2 residues within 4Å: Chain C: G.4, G.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wong, J.H. et al., Structural insight into dynamic bypass of the major cisplatin-DNA adduct by Y-family polymerase Dpo4. Embo J. (2010)

Release Date

2010-06-16

Peptides

DNA polymerase IV: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

DNA polymerase IV

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