SMTL ID : 9gjw.1

OCCM maturation intermediate stalled with an Arginine Finger mutation in Mcm2

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

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

ADP.1: 16 residues within 4Å: Chain A: Y.506, H.508, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, V.699 Chain E: L.565, E.657, Q.658, V.797, R.798, E.801 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain E Hydrogen bonds: A:Y.506, A:Y.506, A:G.546, A:T.547, A:A.548, A:K.549, A:S.550, A:S.550, A:Q.551, A:Q.551, E:E.657 Salt bridges: A:K.549, E:R.798, E:R.798 ADP.2: 12 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 Chain D: R.549 11 PLIP interactions: 1 interactions with chain D, 10 interactions with chain B Salt bridges: D:R.549 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 ADP.4: 18 residues within 4Å: Chain C: S.529, 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.593, P.686, R.687, L.690 11 PLIP interactions: 3 interactions with chain F, 8 interactions with chain C Salt bridges: F:R.593, F:R.687, F:R.687 Hydrogen bonds: C:Y.531, C:Y.531, C:P.570, C:P.570, C:S.573, C:K.574, C:S.575, C:Q.576 ADP.5: 12 residues within 4Å: Chain A: V.807, R.808 Chain D: S.377, I.378, F.379, P.418, G.419, T.420, A.421, K.422, S.423, I.568 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:F.379, D:F.379, D:G.419, D:A.421, D:K.422, D:S.423, D:S.423 Salt bridges: D:K.422, D:K.422, A:R.808 ADP.7: 13 residues within 4Å: Chain C: E.650, T.795, R.796 Chain E: A.536, V.537, F.538, P.577, S.578, T.579, S.580, K.581, S.582, Q.583 13 PLIP interactions: 5 interactions with chain C, 8 interactions with chain E Hydrogen bonds: C:E.650, C:E.650, C:T.795, E:F.538, E:F.538, E:S.580, E:K.581, E:S.582, E:S.582 Salt bridges: C:R.796, C:R.796, E:K.581, E:K.581 ADP.10: 16 residues within 4Å: Chain B: A.734, R.735, E.738 Chain F: E.421, I.422, Y.423, D.461, P.462, G.463, A.465, K.466, S.467, Q.468, N.568, L.612, V.616 16 PLIP interactions: 13 interactions with chain F, 3 interactions with chain B Hydrogen bonds: F:Y.423, F:Y.423, F:G.463, F:V.464, F:A.465, F:K.466, F:S.467, F:S.467, F:S.467, F:Q.468, F:Q.468, F:N.568, B:R.577 Salt bridges: F:K.466, B:R.735, B:R.735

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 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.6: 5 residues within 4Å: Chain D: C.183, C.186, C.211, S.213, 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.8: 4 residues within 4Å: Chain E: C.311, C.314, C.333, C.338 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.311, E:C.314, E:C.333, E:C.338 ZN.9: 5 residues within 4Å: Chain F: C.262, C.265, C.284, S.286, C.289 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.262, F:C.265, F:C.284, F:C.289

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

ATP.11: 13 residues within 4Å: Chain H: P.485, A.486, P.516, G.517, V.518, G.519, K.520, T.521, L.522, Y.662, R.674, R.739 Chain K: R.267 17 PLIP interactions: 16 interactions with chain H, 1 interactions with chain K Hydrogen bonds: H:A.486, H:G.517, H:V.518, H:G.519, H:K.520, H:T.521, H:T.521, H:L.522, H:Y.662, H:Y.662, H:R.674 Salt bridges: H:K.520, H:K.520, H:R.739, H:R.739, H:R.739, K:R.267 ATP.12: 19 residues within 4Å: Chain K: Y.61, G.62, T.63, G.102, P.103, R.104, Q.105, S.106, Y.107, K.108, T.109, Y.110, D.113, E.218, T.252, P.335, K.338 Chain L: K.151, K.158 15 PLIP interactions: 2 interactions with chain L, 13 interactions with chain K Hydrogen bonds: L:K.158, K:G.102, K:Q.105, K:Y.107, K:K.108, K:T.109, K:T.109, K:Y.110, K:D.113, K:E.218, K:K.338 Salt bridges: L:K.151, K:R.104, K:K.108 pi-Stacking: K:Y.110 ATP.13: 14 residues within 4Å: Chain L: V.8, A.9, Y.38, S.39, G.40, T.41, G.42, K.43, T.44, Y.45, L.171, Y.192, I.200, F.256 11 PLIP interactions: 11 interactions with chain L Hydrogen bonds: L:A.9, L:G.40, L:T.41, L:G.42, L:T.44, L:T.44, L:Y.45 Salt bridges: L:K.43, L:K.43 pi-Stacking: L:Y.45, L:Y.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Butryn, A. et al., Unidirectional MCM translocation away from ORC drives origin licensing. Nat Commun (2025)

Release Date

2025-03-05

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
Cell division cycle protein CDT1: G
Origin recognition complex subunit 1: H
Origin recognition complex subunit 2: I
Origin recognition complex subunit 3: J
Origin recognition complex subunit 4: K
Origin recognition complex subunit 5: L
Origin recognition complex subunit 6: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

B
3

C
4

D
5

E
6

F
7

G
8

H
A

I
B

J
C

K
D

L
E

M
F

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

Cell division cycle protein CDT1

Origin recognition complex subunit 1

Origin recognition complex subunit 2

Origin recognition complex subunit 3

Origin recognition complex subunit 4

Origin recognition complex subunit 5

Origin recognition complex subunit 6

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