SMTL ID : 8s94.1

Structure of C-terminal domains of Walker B mutated MCM8/9 heterohexamer complex with ADP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: I.414, F.415, P.456, G.457, L.458, G.459, K.460, S.461, Q.462, L.605 Chain B: E.432, R.482, I.566, R.567 Ligands: MG.2 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:F.415, A:F.415, A:G.457, A:G.459, A:K.460, A:Q.462, B:R.482 Salt bridges: B:R.567, B:R.567 ADP.3: 13 residues within 4Å: Chain B: F.315, P.354, G.355, T.356, G.357, K.358, S.359, I.501 Chain E: R.586, T.710, R.711, E.714 Ligands: MG.4 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain E Hydrogen bonds: B:F.315, B:G.355, B:T.356, B:G.357, B:K.358, B:S.359, E:T.710 Salt bridges: E:R.711, E:R.711 ADP.5: 12 residues within 4Å: Chain C: F.415, P.456, G.457, L.458, G.459, K.460, S.461, L.605 Chain D: R.482, I.566, R.567 Ligands: MG.6 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:R.482, C:F.415, C:F.415, C:G.457, C:G.459, C:K.460, C:S.461 Salt bridges: D:R.567 ADP.7: 13 residues within 4Å: Chain A: R.586, T.710, R.711, E.714 Chain D: F.315, P.354, G.355, T.356, G.357, K.358, S.359, I.501 Ligands: MG.8 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:F.315, D:G.355, D:T.356, D:G.357, D:K.358, D:S.359 Salt bridges: D:K.358, A:R.586, A:R.711, A:R.711 ADP.9: 14 residues within 4Å: Chain E: I.414, F.415, P.456, G.457, L.458, G.459, K.460, S.461, L.605 Chain F: E.432, R.482, I.566, R.567 Ligands: MG.10 8 PLIP interactions: 3 interactions with chain F, 5 interactions with chain E Hydrogen bonds: F:R.482, E:F.415, E:F.415, E:G.457, E:G.459, E:K.460 Salt bridges: F:R.567, F:R.567 ADP.11: 13 residues within 4Å: Chain C: R.586, T.710, R.711, E.714 Chain F: F.315, P.354, G.355, T.356, G.357, K.358, S.359, I.501 Ligands: MG.12 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain F Hydrogen bonds: C:T.710, F:F.315, F:G.355, F:T.356, F:G.357, F:K.358, F:S.359 Salt bridges: C:R.586, C:R.711, C:R.711

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.461, D.518 Ligands: ADP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.461, A:D.518 MG.4: 3 residues within 4Å: Chain B: S.359, D.414 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: S.461, D.518 Ligands: ADP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.461, C:D.518 MG.8: 3 residues within 4Å: Chain D: S.359, D.414 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain E: S.461, D.518 Ligands: ADP.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:S.461, E:D.518 MG.12: 3 residues within 4Å: Chain F: S.359, D.414 Ligands: ADP.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McKinzey, D.R. et al., Activity, substrate preference and structure of the HsMCM8/9 helicase. Nucleic Acids Res. (2023)

Release Date

2023-06-07

Peptides

DNA helicase MCM8: ACE
DNA helicase MCM9: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
B

B
D

D
F

F
E

DNA helicase MCM8

DNA helicase MCM9

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