SMTL ID : 8s0d.1

H. sapiens MCM bound to double stranded DNA and ORC1-6

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

5 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

AGS.1: 13 residues within 4Å: Chain B: S.484, 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 15 PLIP interactions: 11 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, 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: 3 interactions with chain D, 9 interactions with chain F Hydrogen bonds: D:R.497, D:R.643, F:H.359, F:H.359, F:S.399, F:A.401, F:K.402, F:S.403, F:Q.404, F:Q.404, F:E.461 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 14 PLIP interactions: 11 interactions with chain G, 3 interactions with chain C Hydrogen bonds: 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, C:R.480, C:R.618 Salt bridges: G:K.387, C:R.618 AGS.18: 17 residues within 4Å: Chain M: Q.31, N.36, L.37, F.38, V.40, S.71, G.72, K.73, T.74, M.75, L.192, L.276, R.277, H.280 Chain N: R.143, E.146 Ligands: MG.19 11 PLIP interactions: 10 interactions with chain M, 1 interactions with chain N Hydrogen bonds: M:F.38, M:F.38, M:R.69, M:G.70, M:G.72, M:K.73, M:T.74, M:T.74, N:E.146 Salt bridges: M:R.277, M:R.277 AGS.20: 14 residues within 4Å: Chain N: V.7, L.9, R.11, T.39, A.40, G.42, K.43, T.44, Y.45, V.46, Y.182, L.222, K.223 Ligands: MG.21 9 PLIP interactions: 9 interactions with chain N Hydrogen bonds: N:L.9, N:G.42, N:K.43, N:T.44, N:T.44, N:Y.45, N:Y.182, N:Y.182 Salt bridges: N:K.43

8 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 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain G: S.388 Ligands: AGS.15 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.388 MG.19: 3 residues within 4Å: Chain M: T.74, L.192 Ligands: AGS.18 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.74 MG.21: 2 residues within 4Å: Chain N: T.44 Ligands: AGS.20 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:T.44

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: 4 residues within 4Å: Chain E: C.172, S.174, C.175, C.197 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: 4 interactions with chain E, 10 interactions with chain C Hydrogen bonds: E:R.371, E:Q.464, E:E.614, C:H.310, C:H.310, C:S.350, C:V.351, C:A.352, C:K.353, C:S.354, C:Q.355, C:Q.355 Salt bridges: E:R.611, C:K.353 ADP.7: 15 residues within 4Å: Chain D: S.469, 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 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain G Hydrogen bonds: D:Y.471, D:Y.471, D:G.513, D:S.515, D:K.516, D:S.517, D:S.517, D:S.517, D:Q.518 Salt bridges: G:R.604, G:R.604 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 visualized 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
Origin recognition complex subunit 1: J
Origin recognition complex subunit 2: K
Isoform 2 of Origin recognition complex subunit 3: L
Origin recognition complex subunit 4: M
Origin recognition complex subunit 5: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
2

C
3

D
4

E
5

F
6

G
7

J
A

K
B

L
C

M
D

N
E

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

Origin recognition complex subunit 1

Origin recognition complex subunit 2

Isoform 2 of Origin recognition complex subunit 3

Origin recognition complex subunit 4

Origin recognition complex subunit 5

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