SMTL ID : 6eyc.1

Re-refinement of the MCM2-7 double hexamer using ISOLDE

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: C.341, K.343, C.344, C.364, N.366, C.367, S.369 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.341, A:C.344, A:C.364, A:C.367 ZN.5: 5 residues within 4Å: Chain C: C.349, V.351, C.352, C.371, E.378 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.349, C:C.352, C:C.371 ZN.7: 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.9: 6 residues within 4Å: Chain E: C.311, M.313, C.314, A.316, C.333, C.338 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.314, E:C.333, E:C.338 ZN.11: 4 residues within 4Å: Chain F: C.262, C.265, C.284, S.286 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.262, F:C.265, F:C.284

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

ADP.2: 14 residues within 4Å: Chain A: I.505, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, E.608, N.651, L.695, V.699 Chain E: V.797, R.798 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:A.548, A:K.549, A:S.550, A:Q.551, A:N.651, A:N.651 Salt bridges: A:K.549, A:K.549, E:R.798 ADP.3: 18 residues within 4Å: Chain B: S.370, I.371, Y.372, H.374, P.411, S.412, T.413, A.414, K.415, S.416, Q.417 Chain D: L.406, E.498, Q.499, R.549, I.650, R.651, E.654 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:Y.372, B:Y.372, B:H.374, B:T.413, B:S.416, B:S.416, B:Q.417, D:Q.499 Salt bridges: B:K.415, D:R.549, D:R.651, D:R.651 ADP.4: 18 residues within 4Å: Chain B: L.399, E.491, R.542, A.699, R.700, E.703 Chain F: E.421, I.422, Y.423, P.462, G.463, V.464, A.465, K.466, S.467, Q.468, L.612, V.616 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain F Salt bridges: B:R.542, B:R.700, B:R.700 Hydrogen bonds: F:Y.423, F:G.463, F:V.464, F:A.465, F:K.466, F:S.467 ADP.6: 19 residues within 4Å: Chain C: S.529, I.530, Y.531, L.533, P.570, S.571, T.572, K.574, S.575, Q.576, L.720, L.724 Chain F: M.448, I.450, E.542, R.593, P.686, R.687, L.690 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain F Hydrogen bonds: C:Y.531, C:Y.531, C:S.571, C:T.572, C:S.575, C:S.575, C:Q.576, F:E.542 Salt bridges: F:R.593, F:R.687, F:R.687 ADP.8: 17 residues within 4Å: Chain A: R.676, V.807, R.808, E.811 Chain D: S.377, I.378, F.379, N.381, P.418, G.419, T.420, A.421, K.422, S.423, Q.424, I.568, V.572 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:F.379, D:F.379, D:G.419, D:G.419, D:T.420, D:A.421, D:K.422, D:S.423, D:S.423, D:Q.424 Salt bridges: D:K.422, A:R.676, A:R.808 ADP.10: 18 residues within 4Å: Chain C: Y.558, H.646, Q.651, R.701, T.795, R.796, E.799 Chain E: A.536, V.537, F.538, P.577, S.578, T.579, S.580, K.581, S.582, Q.583, L.727 12 PLIP interactions: 3 interactions with chain C, 9 interactions with chain E Hydrogen bonds: C:R.701, C:R.796, E:F.538, E:F.538, E:S.578, E:T.579, E:T.579, E:S.580, E:S.582, E:Q.583, E:Q.583 Salt bridges: C:R.796

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Croll, T.I., ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr D Struct Biol (2018)

Release Date

2018-06-20

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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