SMTL ID : 8rig.1

Cryo-EM structure of an MCM helicase single hexamer loaded onto dsDNA.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 16 residues within 4Å: Chain A: S.504, I.505, Y.506, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, E.608, N.651, L.695 Chain E: R.798, E.801 Ligands: MG.2 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain E Hydrogen bonds: A:Y.506, A:Y.506, A:G.546, A:T.547, A:T.547, A:A.548, A:K.549, A:S.550, A:S.550, A:Q.551, A:Q.551, A:N.651, E:E.801 Salt bridges: A:K.549, A:K.549, E:R.798, E:R.798 ATP.12: 19 residues within 4Å: Chain C: E.650, R.701, T.795, R.796, E.799 Chain E: V.537, F.538, H.540, D.576, P.577, S.578, T.579, S.580, K.581, S.582, Q.583, N.683, L.727 Ligands: MG.13 16 PLIP interactions: 12 interactions with chain E, 4 interactions with chain C Hydrogen bonds: E:F.538, E:H.540, E:S.578, E:T.579, E:S.580, E:K.581, E:S.582, E:Q.583, E:Q.583, E:N.683 Salt bridges: E:K.581, E:K.581, C:R.701, C:R.796, C:R.796, C:R.796

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.550 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.550 MG.5: 2 residues within 4Å: Chain B: S.451 Ligands: ADP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.451 MG.7: 3 residues within 4Å: Chain C: S.575 Chain F: R.593 Ligands: ADP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.575 MG.10: 2 residues within 4Å: Chain D: S.423 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.423 MG.13: 3 residues within 4Å: Chain E: S.582, D.639 Ligands: ATP.12 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.582 MG.17: 2 residues within 4Å: Chain F: S.467 Ligands: ADP.16 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.467

5 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.341, C.344, C.364, C.367 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.341, A:C.344, A:C.364, A:C.367 ZN.8: 4 residues within 4Å: Chain C: C.349, C.352, C.371, C.376 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.349, C:C.352, C:C.371, C:C.376 ZN.11: 4 residues within 4Å: Chain D: C.183, C.186, C.211, C.236 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.183, D:C.186, D:C.211, D:C.236 ZN.14: 6 residues within 4Å: Chain E: C.311, C.314, A.316, C.333, C.338, N.340 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.311, E:C.314, E:C.333, E:C.338 ZN.15: 4 residues within 4Å: Chain F: C.262, C.265, C.284, C.289 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.262, F:C.265, F:C.284, F:C.289

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

ADP.4: 17 residues within 4Å: Chain B: S.405, I.406, Y.407, P.446, S.447, T.448, A.449, K.450, S.451, Q.452, I.596, V.600 Chain D: E.498, I.650, R.651, E.654 Ligands: MG.5 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:Y.407, B:Y.407, B:S.447, B:T.448, B:A.449, B:K.450, B:S.451, B:S.451, B:Q.452, B:Q.452, D:E.498 Salt bridges: B:K.450, D:R.651 ADP.6: 16 residues within 4Å: Chain C: I.530, Y.531, P.570, S.571, T.572, S.573, K.574, S.575, Q.576, L.720, L.724 Chain F: I.450, E.542, R.687, L.690 Ligands: MG.7 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain F Hydrogen bonds: C:Y.531, C:Y.531, C:S.571, C:T.572, C:S.573, C:S.573, C:K.574, C:S.575, C:S.575, C:Q.576, F:E.542 Salt bridges: C:K.574, F:R.687, F:R.687 ADP.9: 16 residues within 4Å: Chain A: R.676, V.807, R.808, E.811 Chain D: S.377, I.378, F.379, P.418, G.419, T.420, A.421, K.422, S.423, Q.424, V.572 Ligands: MG.10 14 PLIP interactions: 11 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:F.379, D:F.379, D:N.381, D:D.417, D:G.419, D:T.420, D:A.421, D:K.422, D:S.423, D:Q.424, A:H.531, A:R.676 Salt bridges: D:K.422, A:R.808 ADP.16: 18 residues within 4Å: Chain B: L.434, E.526, Q.527, A.734, R.735, E.738 Chain F: E.421, I.422, Y.423, G.463, V.464, A.465, K.466, S.467, Q.468, L.612, V.616 Ligands: MG.17 14 PLIP interactions: 4 interactions with chain B, 10 interactions with chain F Hydrogen bonds: B:E.526, B:E.738, F:Y.423, F:Y.423, F:G.463, F:V.464, F:A.465, F:K.466, F:S.467, F:Q.468, F:Q.468 Salt bridges: B:R.735, B:R.735, F:K.466

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller, T.C.R. et al., Inhibition of Origin Recognition Complex by Cyclin Dependent Kinase Reveals Alternate Mechanism of MCM Loading. To Be Published

Release Date

2025-01-01

Peptides

DNA replication licensing factor MCM2: A
DNA replication licensing factor MCM3: B
DNA replication licensing factor MCM4: C
Minichromosome maintenance protein 5: D
DNA replication licensing factor MCM6: E
DNA replication licensing factor MCM7: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

B
3

C
4

D
5

E
6

F
7

DNA replication licensing factor MCM2

DNA replication licensing factor MCM3

DNA replication licensing factor MCM4

Minichromosome maintenance protein 5

DNA replication licensing factor MCM6

DNA replication licensing factor MCM7

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