SMTL ID : 8s0b.1

H. sapiens MCM bound to double stranded DNA and ORC6 as part of the MCM-ORC complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

AGS.1: 12 residues within 4Å: Chain B: Y.486, H.488, G.526, T.527, A.528, K.529, S.530, Q.531, L.675 Chain F: R.619, E.622 Ligands: MG.2 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain F Hydrogen bonds: B:Y.486, B:Y.486, B:G.526, B:T.527, B:A.528, B:K.529, B:K.529, B:S.530, B:Q.531, B:Q.531, B:N.631, F:R.619, F:E.622 Salt bridges: B:K.529, F:R.619, F:R.619 AGS.11: 16 residues within 4Å: Chain D: R.497, E.592, T.639, R.643, R.732, E.735 Chain F: H.359, S.399, T.400, A.401, K.402, S.403, Q.404, E.461, N.504 Ligands: MG.12 12 PLIP interactions: 5 interactions with chain D, 7 interactions with chain F Hydrogen bonds: D:R.497, D:R.497, D:R.643, D:E.735, F:H.359, F:H.359, F:S.399, F:K.402, F:S.403, F:Q.404, F:N.504 Salt bridges: D:R.732 AGS.15: 15 residues within 4Å: Chain C: R.480, A.617, R.618, E.621 Chain G: I.344, Y.345, G.384, V.385, A.386, K.387, S.388, Q.389, N.489, L.533 Ligands: MG.16 15 PLIP interactions: 3 interactions with chain C, 12 interactions with chain G Hydrogen bonds: C:R.480, C:R.618, G:Y.345, G:Y.345, G:G.384, G:V.385, G:A.386, G:K.387, G:S.388, G:S.388, G:Q.389, G:Q.389, G:E.446 Salt bridges: C:R.618, G:K.387

6 x MG: MAGNESIUM ION

MG.2: 2 residues within 4Å: Chain B: S.530 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.530 MG.5: 2 residues within 4Å: Chain C: S.354, D.411 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.354, C:D.411, C:D.411 MG.9: 3 residues within 4Å: Chain E: S.388, D.445 Ligands: ADP.8 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.388 MG.12: 3 residues within 4Å: Chain F: S.403, D.460 Ligands: AGS.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.403 MG.14: 3 residues within 4Å: Chain D: S.517 Chain G: E.463 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:E.463 MG.16: 3 residues within 4Å: Chain G: S.388, D.445 Ligands: AGS.15 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.388

5 x ZN: ZINC ION

ZN.3: 4 residues within 4Å: Chain B: C.329, C.332, C.352, C.355 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.329, B:C.332, B:C.352, B:C.355 ZN.6: 4 residues within 4Å: Chain D: C.306, C.309, C.328, C.331 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.306, D:C.309, D:C.328, D:C.331 ZN.10: 5 residues within 4Å: Chain E: C.172, S.174, C.175, C.197, C.207 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.172, E:C.175, E:C.197 ZN.13: 4 residues within 4Å: Chain F: C.158, C.161, C.180, C.185 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.158, F:C.161, F:C.180, F:C.185 ZN.17: 5 residues within 4Å: Chain G: C.184, C.187, C.206, S.208, C.211 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:C.184, G:C.187, G:C.206, G:S.208, G:C.211

3 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.4: 15 residues within 4Å: Chain C: S.308, I.309, H.310, D.348, P.349, S.350, V.351, A.352, K.353, S.354, Q.355 Chain E: R.371, E.463, R.611, E.614 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain E Hydrogen bonds: C:H.310, C:H.310, C:D.348, C:S.350, C:V.351, C:A.352, C:K.353, C:S.354, C:Q.355, C:Q.355, E:R.371, E:E.614 Salt bridges: C:K.353, E:R.611 ADP.7: 16 residues within 4Å: Chain D: S.469, I.470, Y.471, H.473, P.512, G.513, T.514, S.515, K.516, S.517, Q.518, L.662, L.666 Chain G: E.463, R.604 Ligands: MG.14 13 PLIP interactions: 2 interactions with chain G, 11 interactions with chain D Salt bridges: G:R.604, G:R.604, D:K.516 Hydrogen bonds: D:Y.471, D:Y.471, D:G.513, D:S.515, D:S.515, D:K.516, D:S.517, D:S.517, D:S.517, D:Q.518 ADP.8: 12 residues within 4Å: Chain B: R.656, V.764, E.768 Chain E: S.342, I.343, F.344, P.383, G.384, A.386, K.387, S.388 Ligands: MG.9 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain E Salt bridges: B:R.656, E:K.387 Hydrogen bonds: E:F.344, E:F.344, E:G.384, E:A.386, E:K.387, E:S.388

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weissmann, F. et al., MCM Double Hexamer Loading Visualised with Human Proteins. Nature (2024)

Release Date

2024-10-02

Peptides

Origin recognition complex subunit 6: A
DNA replication licensing factor MCM2: B
DNA replication licensing factor MCM3: C
DNA replication licensing factor MCM4: D
DNA replication licensing factor MCM5: E
DNA replication licensing factor MCM6: F
DNA replication licensing factor MCM7: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
2

C
3

D
4

E
5

F
6

G
7

Origin recognition complex subunit 6

DNA replication licensing factor MCM2

DNA replication licensing factor MCM3

DNA replication licensing factor MCM4

DNA replication licensing factor MCM5

DNA replication licensing factor MCM6

DNA replication licensing factor MCM7

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