SMTL ID : 8s0e.1

H. sapiens OCCM bound to double stranded DNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

5 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 18 residues within 4Å: Chain E: Y.486, H.488, P.525, G.526, T.527, A.528, K.529, S.530, Q.531, V.679 Chain G: L.386, E.478, P.525, R.529, V.618, R.619, E.622 Ligands: MG.2 12 PLIP interactions: 4 interactions with chain G, 8 interactions with chain E Hydrogen bonds: G:R.529, G:R.529, G:R.619, E:Y.486, E:H.488, E:G.526, E:T.527, E:T.527, E:A.528, E:K.529, E:S.530 Salt bridges: G:R.619 AGS.4: 18 residues within 4Å: Chain F: R.497, F.500, E.592, R.643, P.731, R.732, E.735 Chain G: T.357, I.358, H.359, P.398, S.399, T.400, A.401, K.402, S.403, Q.404 Ligands: MG.5 19 PLIP interactions: 10 interactions with chain G, 9 interactions with chain F Hydrogen bonds: G:H.359, G:H.359, G:S.399, G:T.400, G:T.400, G:K.402, G:S.403, G:S.403, G:Q.404, F:R.497, F:R.497, F:E.592, F:R.643, F:R.643, F:R.732, F:R.732 Salt bridges: G:K.402, F:R.732, F:R.732 AGS.6: 15 residues within 4Å: Chain M: V.497, L.504, P.536, G.537, T.538, G.539, K.540, T.541, A.542, Y.681, I.689, R.693, R.720 Chain N: R.209 Ligands: MG.7 15 PLIP interactions: 14 interactions with chain M, 1 interactions with chain N Hydrogen bonds: M:V.497, M:G.537, M:T.538, M:T.538, M:G.539, M:K.540, M:T.541, M:A.542, M:Y.681, M:R.693, M:R.720, M:R.720, N:R.209 Salt bridges: M:K.540, M:R.720 AGS.8: 16 residues within 4Å: Chain N: Q.31, N.36, L.37, F.38, V.40, R.69, G.70, S.71, G.72, K.73, T.74, M.75, L.276, R.277, H.280 Ligands: MG.9 11 PLIP interactions: 11 interactions with chain N Hydrogen bonds: N:F.38, N:F.38, N:R.69, N:G.70, N:G.72, N:K.73, N:T.74, N:T.74, N:M.75 Salt bridges: N:R.277, N:R.277 AGS.10: 14 residues within 4Å: Chain O: V.7, V.8, L.9, R.11, T.39, S.41, G.42, K.43, T.44, Y.45, Y.182, L.222, K.223 Ligands: MG.11 10 PLIP interactions: 10 interactions with chain O Hydrogen bonds: O:L.9, O:L.9, O:S.41, O:G.42, O:K.43, O:T.44, O:Y.45, O:Y.182 Salt bridges: O:K.43, O:K.223

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain E: S.530 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.530 MG.5: 2 residues within 4Å: Chain G: S.403 Ligands: AGS.4 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.403 MG.7: 2 residues within 4Å: Chain M: T.541 Ligands: AGS.6 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.541 MG.9: 2 residues within 4Å: Chain N: T.74 Ligands: AGS.8 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:T.74 MG.11: 2 residues within 4Å: Chain O: T.44 Ligands: AGS.10 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:T.44

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain F: C.306, C.309, C.328, C.331 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.306, F:C.309, F:C.328, F:C.331

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

DNA replication licensing factor MCM5: C
DNA replication factor Cdt1: D
DNA replication licensing factor MCM2: E
DNA replication licensing factor MCM4: F
DNA replication licensing factor MCM6: G
DNA replication licensing factor MCM7: H
Origin recognition complex subunit 2: I
Origin recognition complex subunit 3: J
Cell division control protein 6 homolog: K
DNA replication licensing factor MCM3: L
Origin recognition complex subunit 1: M
Origin recognition complex subunit 4: N
Origin recognition complex subunit 5: O

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
5

D
8

E
2

F
4

G
6

H
7

I
B

J
C

K
G

L
3

M
A

N
D

O
E

DNA replication licensing factor MCM5

DNA replication factor Cdt1

DNA replication licensing factor MCM2

DNA replication licensing factor MCM4

DNA replication licensing factor MCM6

DNA replication licensing factor MCM7

Origin recognition complex subunit 2

Origin recognition complex subunit 3

Cell division control protein 6 homolog

DNA replication licensing factor MCM3

Origin recognition complex subunit 1

Origin recognition complex subunit 4

Origin recognition complex subunit 5

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