SMTL ID : 7pt6.1

Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ATPgS, state III

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x UNK- UNK- UNK- UNK: Undefined Mcm4 flexible N-terminal tail(Non-covalent)

UNK-UNK-UNK-UNK.1: 7 residues within 4Å: Chain G: T.43, F.44, K.165, L.185, G.280, T.281 Chain H: G.511 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:K.165, G:G.280 UNK-UNK-UNK-UNK.2: 8 residues within 4Å: Chain O: T.43, F.44, K.165, L.185, G.280, T.281 Chain P: G.511, L.512 4 PLIP interactions: 4 interactions with chain O Hydrophobic interactions: O:F.44, O:L.185 Hydrogen bonds: O:K.165, O:G.280

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

AGS.3: 18 residues within 4Å: Chain A: S.504, I.505, Y.506, H.508, D.544, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, N.651, L.695 Chain E: V.797, R.798, E.801 Ligands: MG.4 16 PLIP interactions: 13 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:K.549, A:S.550, A:S.550, A:Q.551, A:N.651, A:N.651, E:E.801 Salt bridges: A:K.549, E:R.798, E:R.798 AGS.9: 20 residues within 4Å: Chain C: I.530, Y.531, P.570, S.571, T.572, S.573, K.574, S.575, Q.576, L.720, L.724 Chain F: M.448, I.450, E.542, A.589, R.593, P.686, R.687, L.690 Ligands: MG.17 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain F Hydrogen bonds: C:Y.531, C:S.571, C:T.572, C:T.572, C:S.573, C:S.573, C:K.574, C:K.574, C:S.575, C:S.575, C:Q.576, C:Q.576, F:E.542 Salt bridges: C:K.574, F:R.687, F:R.687 AGS.11: 22 residues within 4Å: Chain A: H.531, E.625, R.676, V.807, R.808, E.811 Chain D: S.377, I.378, F.379, D.417, P.418, G.419, T.420, A.421, K.422, S.423, Q.424, D.480, E.481, N.524, V.572 Ligands: MG.6 14 PLIP interactions: 10 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:F.379, D:F.379, D:G.419, D:T.420, D:A.421, D:K.422, D:S.423, D:Q.424, D:E.481, A:H.531, A:R.676, A:R.808 Salt bridges: D:K.422, A:R.808 AGS.13: 16 residues within 4Å: Chain A: R.326, P.403, R.404, H.405, K.441, N.442 Chain E: T.297, S.298, E.299, R.301, W.356, K.358, Y.621, T.622, I.623, I.668 12 PLIP interactions: 6 interactions with chain E, 6 interactions with chain A Hydrogen bonds: E:E.299, E:K.358, E:T.622, E:I.623, E:G.667, A:R.326, A:P.403, A:R.404, A:K.441, A:N.442 Salt bridges: E:R.301 pi-Stacking: A:H.405 AGS.14: 21 residues within 4Å: Chain C: E.650, P.697, R.701, T.795, R.796, E.799 Chain E: A.536, V.537, F.538, H.540, P.577, S.578, T.579, S.580, K.581, S.582, Q.583, N.683, L.727, I.731 Ligands: MG.15 18 PLIP interactions: 13 interactions with chain E, 5 interactions with chain C Hydrogen bonds: E:F.538, E:F.538, E:S.578, E:T.579, E:S.580, E:K.581, E:K.581, E:S.582, E:S.582, E:Q.583, E:N.683, E:N.683, C:R.701, C:R.701, C:R.796 Salt bridges: E:K.581, C:R.796, C:R.796 AGS.21: 22 residues within 4Å: Chain G: I.39, E.41, G.42, T.43, F.44, S.45, V.47, A.74, K.76, L.120, P.121, Y.122, Y.123, H.125, D.163, K.165, T.167, N.168, L.170, V.181, D.182 Ligands: MG.22 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:T.43, G:F.44, G:S.45, G:P.121, G:Y.123, G:K.165, G:N.168, G:N.168 Salt bridges: G:K.76, G:K.76 AGS.25: 18 residues within 4Å: Chain I: S.504, I.505, Y.506, H.508, D.544, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, N.651, L.695 Chain M: V.797, R.798, E.801 Ligands: MG.26 16 PLIP interactions: 13 interactions with chain I, 3 interactions with chain M Hydrogen bonds: I:Y.506, I:Y.506, I:G.546, I:T.547, I:A.548, I:K.549, I:K.549, I:S.550, I:S.550, I:Q.551, I:N.651, I:N.651, M:E.801 Salt bridges: I:K.549, M:R.798, M:R.798 AGS.31: 20 residues within 4Å: Chain K: I.530, Y.531, P.570, S.571, T.572, S.573, K.574, S.575, Q.576, L.720, L.724 Chain N: M.448, I.450, E.542, A.589, R.593, P.686, R.687, L.690 Ligands: MG.39 16 PLIP interactions: 13 interactions with chain K, 3 interactions with chain N Hydrogen bonds: K:Y.531, K:S.571, K:T.572, K:T.572, K:S.573, K:S.573, K:K.574, K:K.574, K:S.575, K:S.575, K:Q.576, K:Q.576, N:E.542 Salt bridges: K:K.574, N:R.687, N:R.687 AGS.33: 22 residues within 4Å: Chain I: H.531, E.625, R.676, V.807, R.808, E.811 Chain L: S.377, I.378, F.379, D.417, P.418, G.419, T.420, A.421, K.422, S.423, Q.424, D.480, E.481, N.524, V.572 Ligands: MG.28 16 PLIP interactions: 12 interactions with chain L, 4 interactions with chain I Hydrogen bonds: L:F.379, L:F.379, L:G.419, L:T.420, L:A.421, L:K.422, L:S.423, L:S.423, L:Q.424, L:E.481, L:N.524, I:H.531, I:R.676, I:R.808 Salt bridges: L:K.422, I:R.808 AGS.35: 16 residues within 4Å: Chain I: R.326, P.403, R.404, H.405, K.441, N.442 Chain M: T.297, S.298, E.299, R.301, W.356, K.358, Y.621, T.622, I.623, I.668 12 PLIP interactions: 6 interactions with chain I, 6 interactions with chain M Hydrogen bonds: I:R.326, I:P.403, I:R.404, I:K.441, I:N.442, M:E.299, M:K.358, M:T.622, M:I.623, M:G.667 pi-Stacking: I:H.405 Salt bridges: M:R.301 AGS.36: 21 residues within 4Å: Chain K: E.650, P.697, R.701, T.795, R.796, E.799 Chain M: A.536, V.537, F.538, H.540, P.577, S.578, T.579, S.580, K.581, S.582, Q.583, N.683, L.727, I.731 Ligands: MG.37 18 PLIP interactions: 13 interactions with chain M, 5 interactions with chain K Hydrogen bonds: M:F.538, M:F.538, M:S.578, M:T.579, M:S.580, M:K.581, M:K.581, M:S.582, M:S.582, M:Q.583, M:N.683, M:N.683, K:R.701, K:R.701, K:R.796 Salt bridges: M:K.581, K:R.796, K:R.796 AGS.43: 22 residues within 4Å: Chain O: I.39, E.41, G.42, T.43, F.44, S.45, V.47, A.74, K.76, L.120, P.121, Y.122, Y.123, H.125, D.163, K.165, T.167, N.168, L.170, V.181, D.182 Ligands: MG.44 10 PLIP interactions: 10 interactions with chain O Hydrogen bonds: O:T.43, O:F.44, O:S.45, O:P.121, O:Y.123, O:K.165, O:N.168, O:N.168 Salt bridges: O:K.76, O:K.76

14 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: S.550, D.607 Ligands: AGS.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.550 MG.6: 5 residues within 4Å: Chain A: E.625, R.676 Chain D: S.423, D.480 Ligands: AGS.11 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Metal complexes: D:S.423, A:E.625, A:E.625 MG.8: 5 residues within 4Å: Chain B: S.416, D.473, E.474 Chain D: R.549 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.416 MG.15: 4 residues within 4Å: Chain C: R.701 Chain E: S.582, D.639 Ligands: AGS.14 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.582 MG.17: 5 residues within 4Å: Chain C: S.575, D.632 Chain F: E.542, R.593 Ligands: AGS.9 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F Metal complexes: C:S.575, F:E.542 MG.19: 4 residues within 4Å: Chain B: R.542 Chain F: S.467, D.524 Ligands: ADP.18 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.467 MG.22: 2 residues within 4Å: Chain G: D.182 Ligands: AGS.21 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.182, G:D.182 MG.26: 3 residues within 4Å: Chain I: S.550, D.607 Ligands: AGS.25 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:S.550 MG.28: 5 residues within 4Å: Chain I: E.625, R.676 Chain L: S.423, D.480 Ligands: AGS.33 3 PLIP interactions: 1 interactions with chain L, 2 interactions with chain I Metal complexes: L:S.423, I:E.625, I:E.625 MG.30: 5 residues within 4Å: Chain J: S.416, D.473, E.474 Chain L: R.549 Ligands: ADP.29 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:S.416 MG.37: 4 residues within 4Å: Chain K: R.701 Chain M: S.582, D.639 Ligands: AGS.36 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:S.582 MG.39: 5 residues within 4Å: Chain K: S.575, D.632 Chain N: E.542, R.593 Ligands: AGS.31 2 PLIP interactions: 1 interactions with chain N, 1 interactions with chain K Metal complexes: N:E.542, K:S.575 MG.41: 4 residues within 4Å: Chain J: R.542 Chain N: S.467, D.524 Ligands: ADP.40 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:S.467 MG.44: 2 residues within 4Å: Chain O: D.182 Ligands: AGS.43 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:D.182, O:D.182

14 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: C.341, C.344, C.364, C.367 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.341, A:C.344, A:C.364, A:C.367 ZN.10: 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.12: 5 residues within 4Å: Chain D: C.183, N.185, C.186, C.211, 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.16: 5 residues within 4Å: Chain E: C.311, C.314, C.333, C.338, N.340 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.311, E:C.314, E:C.333, E:C.338 ZN.20: 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 ZN.23: 4 residues within 4Å: Chain G: C.223, C.225, C.293, H.348 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.223, G:C.225, G:C.293, G:H.348 ZN.24: 5 residues within 4Å: Chain H: C.661, N.663, C.664, H.674, H.680 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.661, H:C.664, H:H.674, H:H.680 ZN.27: 4 residues within 4Å: Chain I: C.341, C.344, C.364, C.367 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.341, I:C.344, I:C.364, I:C.367 ZN.32: 4 residues within 4Å: Chain K: C.349, C.352, C.371, C.376 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.349, K:C.352, K:C.371, K:C.376 ZN.34: 5 residues within 4Å: Chain L: C.183, N.185, C.186, C.211, C.236 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.183, L:C.186, L:C.211, L:C.236 ZN.38: 5 residues within 4Å: Chain M: C.311, C.314, C.333, C.338, N.340 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.311, M:C.314, M:C.333, M:C.338 ZN.42: 5 residues within 4Å: Chain N: C.262, C.265, C.284, S.286, C.289 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.262, N:C.265, N:C.284, N:C.289 ZN.45: 4 residues within 4Å: Chain O: C.223, C.225, C.293, H.348 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.223, O:C.225, O:C.293, O:H.348 ZN.46: 5 residues within 4Å: Chain P: C.661, N.663, C.664, H.674, H.680 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.661, P:C.664, P:H.674, P:H.680

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

ADP.7: 18 residues within 4Å: Chain B: S.370, I.371, Y.372, D.410, P.411, S.412, T.413, A.414, K.415, S.416, Q.417 Chain D: E.498, Q.499, R.549, I.650, R.651, E.654 Ligands: MG.8 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain D Hydrogen bonds: B:Y.372, B:Y.372, B:D.410, B:S.412, B:T.413, B:A.414, B:K.415, B:S.416, B:Q.417, D:E.498, D:Q.499 Salt bridges: B:K.415, D:R.549, D:R.651, D:R.651 ADP.18: 19 residues within 4Å: Chain B: E.491, Q.492, A.699, R.700, E.703 Chain F: E.421, I.422, Y.423, D.461, P.462, G.463, V.464, A.465, K.466, S.467, Q.468, L.612, V.616 Ligands: MG.19 15 PLIP interactions: 5 interactions with chain B, 10 interactions with chain F Hydrogen bonds: B:E.491, B:Q.492, B:Q.492, F:Y.423, F:Y.423, F:N.425, F:G.463, F:V.464, F:A.465, F:K.466, F:S.467, F:Q.468 Salt bridges: B:R.700, B:R.700, F:K.466 ADP.29: 18 residues within 4Å: Chain J: S.370, I.371, Y.372, D.410, P.411, S.412, T.413, A.414, K.415, S.416, Q.417 Chain L: E.498, Q.499, R.549, I.650, R.651, E.654 Ligands: MG.30 15 PLIP interactions: 5 interactions with chain L, 10 interactions with chain J Hydrogen bonds: L:E.498, L:Q.499, J:Y.372, J:Y.372, J:D.410, J:S.412, J:T.413, J:A.414, J:K.415, J:S.416, J:Q.417 Salt bridges: L:R.549, L:R.651, L:R.651, J:K.415 ADP.40: 19 residues within 4Å: Chain J: E.491, Q.492, A.699, R.700, E.703 Chain N: E.421, I.422, Y.423, D.461, P.462, G.463, V.464, A.465, K.466, S.467, Q.468, L.612, V.616 Ligands: MG.41 15 PLIP interactions: 10 interactions with chain N, 5 interactions with chain J Hydrogen bonds: N:Y.423, N:Y.423, N:N.425, N:G.463, N:V.464, N:A.465, N:K.466, N:S.467, N:Q.468, J:E.491, J:Q.492, J:Q.492 Salt bridges: N:K.466, J:R.700, J:R.700

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saleh, A. et al., The structural basis of Cdc7-Dbf4 kinase dependent targeting and phosphorylation of the MCM2-7 double hexamer. Nat Commun (2022)

Release Date

2022-06-08

Peptides

DNA replication licensing factor MCM2: AI
DNA replication licensing factor MCM3: BJ
DNA replication licensing factor MCM4: CK
Minichromosome maintenance protein 5: DL
DNA replication licensing factor MCM6: EM
DNA replication licensing factor MCM7: FN
Cell division control protein 7: GO
DDK kinase regulatory subunit DBF4: HP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

I
B

B
3

J
C

C
4

K
D

D
5

L
E

E
6

M
F

F
7

N
G

G
8

O
H

H
9

P
I

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 control protein 7

DDK kinase regulatory subunit DBF4

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