SMTL ID : 7w1y.1

Human MCM double hexamer bound to natural DNA duplex (polyAT/polyTA)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-mer

Ligands

10 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.329, C.332, C.352, C.355 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.329, A:C.332, A:C.352, A:C.355 ZN.6: 4 residues within 4Å: Chain C: C.306, C.309, C.328, C.331 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.306, C:C.309, C:C.328, C:C.331 ZN.9: 4 residues within 4Å: Chain D: C.172, C.175, C.197, C.207 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.172, D:C.175, D:C.197, D:C.207 ZN.12: 4 residues within 4Å: Chain E: C.158, C.161, C.180, C.185 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.158, E:C.161, E:C.180, E:C.185 ZN.15: 4 residues within 4Å: Chain F: C.184, C.187, C.206, C.211 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.184, F:C.187, F:C.206, F:C.211 ZN.18: 4 residues within 4Å: Chain G: C.329, C.332, C.352, C.355 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.329, G:C.332, G:C.352, G:C.355 ZN.23: 4 residues within 4Å: Chain I: C.306, C.309, C.328, C.331 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.306, I:C.309, I:C.328, I:C.331 ZN.26: 6 residues within 4Å: Chain J: C.172, S.174, C.175, C.197, T.199, C.207 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.172, J:C.175, J:C.197, J:C.207 ZN.29: 4 residues within 4Å: Chain K: C.158, C.161, C.180, C.185 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.158, K:C.161, K:C.180, K:C.185 ZN.32: 5 residues within 4Å: Chain L: C.184, C.187, C.206, S.208, C.211 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.184, L:C.187, L:C.206, L:C.211

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.530, D.587 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.530 MG.4: 3 residues within 4Å: Chain B: S.397, E.455 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.397 MG.7: 3 residues within 4Å: Chain C: S.517 Chain F: R.514 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.517 MG.10: 4 residues within 4Å: Chain D: S.388, D.445, E.446 Ligands: ADP.11 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.388 MG.13: 5 residues within 4Å: Chain C: R.643 Chain E: S.403, D.460, E.461 Ligands: ADP.14 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.403 MG.16: 3 residues within 4Å: Chain B: R.523 Chain F: S.388 Ligands: ATP.17 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.388 MG.19: 3 residues within 4Å: Chain G: S.530, D.587 Ligands: ATP.20 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.530 MG.21: 3 residues within 4Å: Chain H: S.397 Chain J: R.513 Ligands: ATP.22 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:S.397 MG.24: 5 residues within 4Å: Chain I: S.517, D.574, E.575 Chain L: R.514 Ligands: ATP.25 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:S.517 MG.27: 5 residues within 4Å: Chain G: E.605 Chain J: S.388, D.445, E.446 Ligands: ADP.28 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:S.388 MG.30: 4 residues within 4Å: Chain I: E.592 Chain K: S.403, E.461 Ligands: ADP.31 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:S.403 MG.33: 4 residues within 4Å: Chain L: S.388, D.445, E.446 Ligands: ATP.34 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:S.388

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

ATP.3: 17 residues within 4Å: Chain A: I.485, Y.486, H.488, P.525, G.526, T.527, A.528, K.529, S.530, Q.531, N.631, L.675, V.679 Chain E: V.618, R.619, E.622 Ligands: MG.2 15 PLIP interactions: 3 interactions with chain E, 12 interactions with chain A Salt bridges: E:R.619, E:R.619, E:R.619, A:K.529, A:K.529 Hydrogen bonds: A:Y.486, A:Y.486, A:G.526, A:T.527, A:A.528, A:K.529, A:S.530, A:S.530, A:Q.531, A:N.631 ATP.5: 22 residues within 4Å: Chain B: S.351, I.352, H.353, P.392, S.393, V.394, A.395, K.396, S.397, Q.398, E.455, N.498, I.542 Chain D: R.371, E.463, Q.464, T.509, R.513, V.610, R.611, E.614 Ligands: MG.4 18 PLIP interactions: 12 interactions with chain B, 6 interactions with chain D Hydrogen bonds: B:H.353, B:H.353, B:S.393, B:V.394, B:A.395, B:K.396, B:S.397, B:S.397, B:Q.398, B:N.498, D:E.463, D:E.463 Salt bridges: B:K.396, B:K.396, D:R.513, D:R.611, D:R.611, D:R.611 ATP.8: 21 residues within 4Å: Chain C: Y.471, H.473, P.512, G.513, T.514, S.515, K.516, S.517, Q.518, E.575, N.618, Y.658, L.662, L.666 Chain F: M.369, I.371, E.463, R.514, R.604, L.607 Ligands: MG.7 19 PLIP interactions: 12 interactions with chain C, 7 interactions with chain F Hydrogen bonds: C:Y.471, C:G.513, C:T.514, C:S.515, C:K.516, C:S.517, C:Q.518, C:N.618, C:Y.658, C:Y.658, F:E.463, F:E.463, F:Q.464 Salt bridges: C:K.516, C:K.516, F:R.514, F:R.604, F:R.604, F:R.604 ATP.17: 23 residues within 4Å: Chain B: I.380, E.472, Q.473, R.523, A.660, R.661, E.664 Chain F: E.343, I.344, Y.345, D.382, P.383, G.384, V.385, A.386, K.387, S.388, Q.389, E.446, N.489, L.533, I.537 Ligands: MG.16 17 PLIP interactions: 5 interactions with chain B, 12 interactions with chain F Hydrogen bonds: B:E.472, F:Y.345, F:Y.345, F:G.384, F:V.385, F:A.386, F:K.387, F:S.388, F:Q.389, F:N.489, F:N.489 Salt bridges: B:R.523, B:R.661, B:R.661, B:R.661, F:K.387, F:K.387 ATP.20: 18 residues within 4Å: Chain G: S.484, I.485, Y.486, H.488, P.525, G.526, T.527, A.528, K.529, S.530, Q.531, N.631, L.675 Chain K: S.528, V.618, R.619, E.622 Ligands: MG.19 18 PLIP interactions: 13 interactions with chain G, 5 interactions with chain K Hydrogen bonds: G:Y.486, G:Y.486, G:G.526, G:T.527, G:T.527, G:A.528, G:K.529, G:S.530, G:Q.531, G:Q.531, G:N.631, K:S.528, K:E.622 Salt bridges: G:K.529, G:K.529, K:R.619, K:R.619, K:R.619 ATP.22: 24 residues within 4Å: Chain H: S.351, I.352, H.353, D.391, P.392, S.393, V.394, A.395, K.396, S.397, Q.398, E.455, N.498, I.542, V.546 Chain J: R.371, E.463, Q.464, T.509, R.513, V.610, R.611, E.614 Ligands: MG.21 21 PLIP interactions: 7 interactions with chain J, 14 interactions with chain H Hydrogen bonds: J:R.371, J:E.463, J:Q.464, H:H.353, H:H.353, H:S.393, H:V.394, H:A.395, H:K.396, H:S.397, H:S.397, H:Q.398, H:Q.398, H:N.498, H:N.498 Salt bridges: J:R.513, J:R.611, J:R.611, J:R.611, H:K.396, H:K.396 ATP.25: 25 residues within 4Å: Chain I: S.469, I.470, Y.471, H.473, P.512, G.513, T.514, S.515, K.516, S.517, Q.518, E.575, N.618, Y.658, L.662, L.666 Chain L: M.369, E.463, Q.464, A.510, R.514, A.603, R.604, L.607 Ligands: MG.24 17 PLIP interactions: 4 interactions with chain L, 13 interactions with chain I Salt bridges: L:R.514, L:R.604, L:R.604, L:R.604, I:K.516, I:K.516 Hydrogen bonds: I:Y.471, I:Y.471, I:G.513, I:T.514, I:T.514, I:S.515, I:K.516, I:S.517, I:Q.518, I:Q.518, I:N.618 ATP.34: 22 residues within 4Å: Chain H: E.472, Q.473, R.523, A.660, R.661, E.664 Chain L: E.343, I.344, Y.345, D.382, P.383, G.384, V.385, A.386, K.387, S.388, Q.389, E.446, N.489, L.533, I.537 Ligands: MG.33 19 PLIP interactions: 12 interactions with chain L, 7 interactions with chain H Hydrogen bonds: L:Y.345, L:Y.345, L:G.384, L:V.385, L:A.386, L:K.387, L:S.388, L:S.388, L:Q.389, L:N.489, H:E.472, H:Q.473, H:E.664 Salt bridges: L:K.387, L:K.387, H:R.523, H:R.661, H:R.661, H:R.661

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

ADP.11: 16 residues within 4Å: Chain A: H.511, R.656, V.764, R.765, E.768 Chain D: F.344, P.383, G.384, T.385, A.386, K.387, S.388, Q.389, M.531, H.535 Ligands: MG.10 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:F.344, D:F.344, D:A.386, D:K.387, D:S.388, D:Q.389, D:Q.389, A:R.656 Salt bridges: D:K.387, D:K.392 pi-Stacking: D:H.535 ADP.14: 16 residues within 4Å: Chain C: R.497, E.592, P.731, R.732, E.735 Chain E: T.357, H.359, P.398, S.399, T.400, A.401, K.402, S.403, Q.404, I.548 Ligands: MG.13 13 PLIP interactions: 9 interactions with chain E, 4 interactions with chain C Hydrogen bonds: E:H.359, E:H.359, E:S.399, E:T.400, E:A.401, E:K.402, E:S.403, E:Q.404, C:R.497, C:E.592 Salt bridges: E:K.402, C:R.732, C:R.732 ADP.28: 16 residues within 4Å: Chain G: H.511, R.656, V.764, E.768 Chain J: S.342, I.343, F.344, P.383, G.384, T.385, A.386, K.387, S.388, Q.389, H.535 Ligands: MG.27 9 PLIP interactions: 2 interactions with chain G, 7 interactions with chain J Hydrogen bonds: G:H.511, G:R.656, J:F.344, J:F.344, J:K.387, J:S.388, J:Q.389 Salt bridges: J:K.387 pi-Cation interactions: J:H.535 ADP.31: 16 residues within 4Å: Chain I: R.497, P.731, R.732, E.735 Chain K: T.357, I.358, H.359, P.398, S.399, T.400, A.401, K.402, S.403, Q.404, I.548 Ligands: MG.30 14 PLIP interactions: 11 interactions with chain K, 3 interactions with chain I Hydrogen bonds: K:H.359, K:H.359, K:N.361, K:S.399, K:T.400, K:T.400, K:A.401, K:K.402, K:S.403, K:Q.404, I:R.497 Salt bridges: K:K.402, I:R.732, I:R.732

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., The human pre-replication complex is an open complex. Cell (2023)

Release Date

2023-02-08

Peptides

DNA replication licensing factor MCM2: AG
Isoform 2 of DNA replication licensing factor MCM3: BH
DNA replication licensing factor MCM4: CI
DNA replication licensing factor MCM5: DJ
DNA replication licensing factor MCM6: EK
DNA replication licensing factor MCM7: FL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

G
A

B
3

H
B

C
4

I
C

D
5

J
D

E
6

K
E

F
7

L
F

DNA replication licensing factor MCM2

Isoform 2 of 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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