SMTL ID : 7pt7.1

Structure of MCM2-7 DH complexed with Cdc7-Dbf4 in the presence of ADP:BeF3, state I

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-1-1-mer

Ligands

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

UNK-UNK-UNK-UNK.1: 6 residues within 4Å: Chain G: T.43, R.278, G.280, R.282 Chain H: G.511 Ligands: BEF.24 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:T.43 Hydrogen bonds: G:G.280, G:R.282, G:R.282

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

ADP.2: 15 residues within 4Å: Chain A: S.504, I.505, Y.506, H.508, P.545, G.546, T.547, A.548, K.549, S.550, L.695 Chain E: V.797, R.798, E.801 Ligands: MG.3 12 PLIP interactions: 9 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:Q.551, E:E.801 Salt bridges: A:K.549, E:R.798, E:R.798 ADP.5: 19 residues within 4Å: Chain B: S.370, I.371, Y.372, P.411, S.412, T.413, A.414, K.415, S.416, Q.417, I.561 Chain D: E.498, Q.499, R.549, I.650, R.651, E.654 Ligands: BEF.6, MG.7 14 PLIP interactions: 4 interactions with chain D, 10 interactions with chain B Hydrogen bonds: D:E.498, D:R.549, B:Y.372, B:Y.372, B:S.412, B:T.413, B:A.414, B:K.415, B:S.416, B:Q.417, B:Q.417 Salt bridges: D:R.651, D:R.651, B:K.415 ADP.10: 19 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 Chain F: M.448, I.450, E.542, Q.543, P.686, R.687, L.690 Ligands: BEF.11, MG.12 12 PLIP interactions: 3 interactions with chain F, 9 interactions with chain C Hydrogen bonds: F:Q.543, C:Y.531, C:Y.531, C:S.571, C:T.572, C:S.573, C:K.574, C:S.575, C:Q.576 Salt bridges: F:R.687, F:R.687, C:K.574 ADP.13: 16 residues within 4Å: Chain A: H.531, R.676, V.807, R.808, E.811 Chain D: S.377, I.378, F.379, P.418, G.419, T.420, A.421, K.422, S.423, Q.424 Ligands: MG.14 15 PLIP interactions: 4 interactions with chain A, 11 interactions with chain D Hydrogen bonds: A:H.531, A:R.676, D:F.379, D:F.379, D:D.417, D:G.419, D:T.420, D:A.421, D:K.422, D:S.423, D:Q.424, D:Q.424 Salt bridges: A:R.808, A:R.808, D:K.422 ADP.16: 21 residues within 4Å: Chain C: Y.558, E.650, R.701, T.795, R.796, E.799 Chain E: A.536, V.537, F.538, H.540, D.576, P.577, S.578, T.579, S.580, K.581, S.582, Q.583, L.727, I.731 Ligands: MG.17 17 PLIP interactions: 12 interactions with chain E, 5 interactions with chain C Hydrogen bonds: E:F.538, E:F.538, E:D.576, E:S.578, E:T.579, E:S.580, E:K.581, E:S.582, E:S.582, E:Q.583, E:Q.583, C:T.795, C:E.799 Salt bridges: E:K.581, C:R.701, C:R.796, C:R.796 ADP.20: 19 residues within 4Å: Chain B: E.491, Q.492, A.699, R.700, E.703 Chain F: E.421, I.422, Y.423, N.425, P.462, G.463, V.464, A.465, K.466, S.467, Q.468, L.612 Ligands: BEF.8, MG.21 16 PLIP interactions: 12 interactions with chain F, 4 interactions with chain B Hydrogen bonds: 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, F:Q.468, F:Q.468, B:E.491, B:Q.492 Salt bridges: F:K.466, B:R.700, B:R.700 ADP.22: 20 residues within 4Å: Chain G: G.40, E.41, G.42, T.43, F.44, S.45, V.47, A.74, K.76, P.121, Y.123, H.125, T.167, N.168, L.170, V.181, D.182 Ligands: MG.23, BEF.24, MG.25 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:F.44, G:S.45, G:P.121, G:Y.123, G:T.167, G:N.168 Salt bridges: G:K.76, G:K.76 ADP.28: 15 residues within 4Å: Chain I: I.505, Y.506, H.508, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, L.695 Chain M: V.797, R.798, E.801 Ligands: MG.29 13 PLIP interactions: 10 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:S.550, I:Q.551, I:Q.551, M:E.801 Salt bridges: I:K.549, M:R.798, M:R.798 ADP.31: 16 residues within 4Å: Chain J: S.370, I.371, Y.372, P.411, S.412, T.413, A.414, K.415, S.416, Q.417 Chain L: E.498, Q.499, I.650, R.651 Ligands: MG.32, BEF.37 15 PLIP interactions: 10 interactions with chain J, 5 interactions with chain L Hydrogen bonds: J:Y.372, J:Y.372, J:S.412, J:T.413, J:A.414, J:K.415, J:S.416, J:Q.417, J:Q.417, L:E.498, L:E.498, L:R.549 Salt bridges: J:K.415, L:R.651, L:R.651 ADP.34: 19 residues within 4Å: Chain K: I.530, Y.531, L.533, P.570, S.571, T.572, S.573, K.574, S.575, Q.576, L.720 Chain N: M.448, I.450, E.542, P.686, R.687, L.690 Ligands: BEF.35, MG.36 13 PLIP interactions: 11 interactions with chain K, 2 interactions with chain N Hydrogen bonds: K:Y.531, K:Y.531, K:S.571, K:T.572, K:S.573, K:S.573, K:K.574, K:S.575, K:S.575, K:Q.576 Salt bridges: K:K.574, N:R.687, N:R.687 ADP.38: 18 residues within 4Å: Chain I: H.531, 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, V.572 Ligands: MG.39 14 PLIP interactions: 10 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, I:H.531, I:R.676 Salt bridges: L:K.422, I:R.808, I:R.808 ADP.41: 18 residues within 4Å: Chain K: 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, L.727, I.731 Ligands: MG.42 14 PLIP interactions: 9 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:S.582, M:Q.583, K:E.650, K:T.795 Salt bridges: M:K.581, K:R.701, K:R.796, K:R.796 ADP.45: 20 residues within 4Å: Chain J: E.491, Q.492, A.699, R.700, E.703 Chain N: E.421, I.422, Y.423, N.425, P.462, G.463, V.464, A.465, K.466, S.467, Q.468, L.612, V.616 Ligands: BEF.46, MG.47 13 PLIP interactions: 9 interactions with chain N, 4 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 Salt bridges: J:R.700, J:R.700

14 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: S.550, D.607, E.608 Ligands: ADP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.550 MG.7: 5 residues within 4Å: Chain B: S.416, D.473, E.474 Ligands: ADP.5, BEF.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.416 MG.12: 5 residues within 4Å: Chain C: S.575, E.633 Chain F: R.593 Ligands: ADP.10, BEF.11 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.575 MG.14: 2 residues within 4Å: Chain D: S.423 Ligands: ADP.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.423 MG.17: 3 residues within 4Å: Chain E: S.582, D.639 Ligands: ADP.16 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.582 MG.21: 5 residues within 4Å: Chain B: R.542 Chain F: S.467, D.524 Ligands: BEF.8, ADP.20 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.467 MG.23: 5 residues within 4Å: Chain G: N.168, D.182 Ligands: ADP.22, BEF.24, MG.25 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.182 MG.25: 6 residues within 4Å: Chain G: D.163, D.182, G.184 Ligands: ADP.22, MG.23, BEF.24 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.182, G:D.182 MG.29: 2 residues within 4Å: Chain I: S.550 Ligands: ADP.28 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:S.550 MG.32: 4 residues within 4Å: Chain J: S.416, E.474 Ligands: ADP.31, BEF.37 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:S.416 MG.36: 5 residues within 4Å: Chain K: S.575, D.632, E.633 Ligands: ADP.34, BEF.35 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:S.575 MG.39: 6 residues within 4Å: Chain I: E.625, R.676 Chain L: S.423, D.480, E.481 Ligands: ADP.38 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:S.423 MG.42: 3 residues within 4Å: Chain M: S.582, D.639 Ligands: ADP.41 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:S.582 MG.47: 5 residues within 4Å: Chain N: S.467, D.524, E.525 Ligands: ADP.45, BEF.46 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:S.467

12 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: C.341, C.344, C.364, C.367, S.369 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.341, A:C.344, A:C.364, A:C.367 ZN.9: 5 residues within 4Å: Chain C: C.349, C.352, C.371, D.375, 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.15: 4 residues within 4Å: Chain D: C.183, 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.18: 6 residues within 4Å: Chain E: C.311, M.313, C.314, C.333, C.338, N.340 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:C.311, E:M.313, E:C.314, E:C.333, E:C.338 ZN.19: 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.26: 5 residues within 4Å: Chain G: C.223, C.225, C.293, G.294, H.348 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:C.223, G:C.223, G:C.225, G:C.293, G:H.348 ZN.27: 4 residues within 4Å: Chain H: C.661, 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.30: 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.33: 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.40: 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.43: 5 residues within 4Å: Chain M: C.311, M.313, C.314, C.333, C.338 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:C.311, M:M.313, M:C.314, M:C.333, M:C.338 ZN.44: 4 residues within 4Å: Chain N: C.262, C.265, C.284, C.289 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.262, N:C.265, N:C.284, N:C.289

7 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.6: 10 residues within 4Å: Chain B: P.411, S.412, K.415, S.416, E.474, N.517 Chain D: R.549, R.651 Ligands: ADP.5, MG.7 No protein-ligand interaction detected (PLIP) BEF.8: 10 residues within 4Å: Chain B: S.538, R.542, R.700 Chain F: P.462, G.463, K.466, S.467, N.568 Ligands: ADP.20, MG.21 No protein-ligand interaction detected (PLIP) BEF.11: 11 residues within 4Å: Chain C: P.570, S.571, K.574, S.575, E.633, N.676 Chain F: A.589, R.593, R.687 Ligands: ADP.10, MG.12 No protein-ligand interaction detected (PLIP) BEF.24: 11 residues within 4Å: Chain G: T.43, F.44, D.163, K.165, N.168, D.182, L.185 Ligands: UNK-UNK-UNK-UNK.1, ADP.22, MG.23, MG.25 No protein-ligand interaction detected (PLIP) BEF.35: 10 residues within 4Å: Chain K: P.570, S.571, K.574, E.633, N.676 Chain N: A.589, R.593, R.687 Ligands: ADP.34, MG.36 No protein-ligand interaction detected (PLIP) BEF.37: 9 residues within 4Å: Chain J: P.411, S.412, K.415, N.517 Chain L: T.545, R.549, R.651 Ligands: ADP.31, MG.32 No protein-ligand interaction detected (PLIP) BEF.46: 11 residues within 4Å: Chain J: S.538, R.542, R.700 Chain N: P.462, G.463, K.466, S.467, E.525, N.568 Ligands: ADP.45, MG.47 No protein-ligand interaction detected (PLIP)

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: G
DDK kinase regulatory subunit DBF4: H

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

H
9

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

Related Entries With Identical Sequence