SMTL ID : 7p5z.1

Structure of a DNA-loaded MCM double hexamer engaged with the Dbf4-dependent kinase

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 18 residues within 4Å: Chain A: I.505, Y.506, H.508, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, N.651, L.695, F.698, V.699 Chain E: V.797, R.798, E.801 Ligands: MG.2 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain E Hydrogen bonds: A:Y.506, A:G.546, A:T.547, A:T.547, A:A.548, A:K.549, A:S.550, A:N.651, E:E.801 Salt bridges: A:K.549, A:K.549, E:R.798, E:R.798 ATP.16: 18 residues within 4Å: Chain G: I.505, Y.506, H.508, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, N.651, L.695, F.698, V.699 Chain K: V.797, R.798, E.801 Ligands: MG.17 14 PLIP interactions: 11 interactions with chain G, 3 interactions with chain K Hydrogen bonds: G:Y.506, G:G.546, G:T.547, G:A.548, G:K.549, G:S.550, G:Q.551, G:N.651, G:N.651, K:E.801 Salt bridges: G:K.549, G:K.549, K:R.798, K:R.798

10 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.550 Chain E: R.798 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.550 MG.5: 3 residues within 4Å: Chain B: K.450, S.451 Ligands: ADP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.451 MG.9: 4 residues within 4Å: Chain A: R.808 Chain D: K.422, S.423 Ligands: ADP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.423 MG.12: 4 residues within 4Å: Chain C: S.575 Chain F: E.542, R.687 Ligands: ADP.6 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C Metal complexes: F:E.542, C:S.575 MG.14: 3 residues within 4Å: Chain F: S.467, D.524 Ligands: ADP.13 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.467 MG.17: 2 residues within 4Å: Chain G: S.550 Ligands: ATP.16 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.550 MG.20: 3 residues within 4Å: Chain H: K.450, S.451 Ligands: ADP.19 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:S.451 MG.24: 4 residues within 4Å: Chain G: R.808 Chain J: K.422, S.423 Ligands: ADP.23 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:S.423 MG.27: 5 residues within 4Å: Chain I: S.575, Q.576 Chain L: E.542, R.687 Ligands: ADP.21 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:S.575 MG.29: 5 residues within 4Å: Chain H: Q.527, R.577 Chain L: S.467, D.524 Ligands: ADP.28 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:S.467

11 x ZN: ZINC ION(Non-covalent)

ZN.3: 7 residues within 4Å: Chain A: C.341, K.343, C.344, S.346, C.364, N.366, 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.7: 7 residues within 4Å: Chain C: C.349, V.351, C.352, H.354, C.371, R.373, 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.10: 6 residues within 4Å: Chain D: C.183, N.185, C.186, H.188, 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.11: 6 residues within 4Å: Chain E: C.311, C.314, A.316, 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.15: 6 residues within 4Å: Chain F: C.262, Q.264, 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.18: 7 residues within 4Å: Chain G: C.341, K.343, C.344, S.346, C.364, N.366, C.367 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.341, G:C.344, G:C.364, G:C.367 ZN.22: 7 residues within 4Å: Chain I: C.349, V.351, C.352, H.354, C.371, R.373, C.376 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.349, I:C.352, I:C.371, I:C.376 ZN.25: 6 residues within 4Å: Chain J: C.183, N.185, C.186, H.188, C.211, C.236 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.183, J:C.186, J:C.211, J:C.236 ZN.26: 6 residues within 4Å: Chain K: C.311, C.314, A.316, C.333, C.338, N.340 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.311, K:C.314, K:C.333, K:C.338 ZN.30: 6 residues within 4Å: Chain L: C.262, Q.264, C.265, C.284, S.286, C.289 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.262, L:C.265, L:C.284, L:C.289 ZN.31: 5 residues within 4Å: Chain N: C.695, N.697, C.698, H.708, H.714 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.695, N:C.698, N:H.708, N:H.714

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

ADP.4: 22 residues within 4Å: Chain B: S.405, I.406, Y.407, H.409, D.445, P.446, S.447, T.448, A.449, K.450, S.451, Q.452, I.596, V.600 Chain D: L.406, E.498, Q.499, R.549, I.650, R.651, E.654 Ligands: MG.5 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:Y.407, B:Y.407, B:D.445, B:T.448, B:A.449, B:K.450, B:S.451, B:S.451, B:Q.452, D:E.654 Salt bridges: B:K.450, D:R.651, D:R.651 ADP.6: 23 residues within 4Å: Chain C: S.529, I.530, Y.531, E.532, L.533, D.569, P.570, S.571, T.572, S.573, K.574, S.575, Q.576, L.720, H.723, L.724 Chain F: I.450, E.542, R.593, P.686, R.687, L.690 Ligands: MG.12 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:Y.531, C:Y.531, C:D.569, C:S.573, C:S.573, C:K.574, C:K.574, C:S.575, C:S.575, C:Q.576 Salt bridges: C:K.574, F:R.687, F:R.687 ADP.8: 20 residues within 4Å: Chain A: H.531, I.533, R.676, V.807, R.808, E.811 Chain D: S.377, I.378, F.379, G.419, T.420, A.421, K.422, S.423, Q.424, I.568, H.571, V.572, I.575 Ligands: MG.9 15 PLIP interactions: 11 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:F.379, D:F.379, D:G.419, D:T.420, D:T.420, D:A.421, D:K.422, D:S.423, D:S.423, D:Q.424, A:R.676, A:E.811 Salt bridges: D:K.422, A:R.808, A:R.808 ADP.13: 21 residues within 4Å: Chain B: L.434, E.526, Q.527, R.577, A.734, R.735, E.738 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, V.616 Ligands: MG.14 14 PLIP interactions: 10 interactions with chain F, 4 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:Q.468, B:Q.527, B:E.738 Salt bridges: F:K.466, B:R.735, B:R.735 ADP.19: 21 residues within 4Å: Chain H: S.405, I.406, Y.407, H.409, D.445, P.446, S.447, T.448, A.449, K.450, S.451, Q.452, V.600 Chain J: L.406, E.498, Q.499, R.549, I.650, R.651, E.654 Ligands: MG.20 13 PLIP interactions: 9 interactions with chain H, 4 interactions with chain J Hydrogen bonds: H:Y.407, H:Y.407, H:D.445, H:T.448, H:A.449, H:K.450, H:S.451, H:Q.452, J:R.549, J:E.654 Salt bridges: H:K.450, J:R.651, J:R.651 ADP.21: 21 residues within 4Å: Chain I: S.529, I.530, Y.531, L.533, P.570, S.571, T.572, S.573, K.574, S.575, Q.576, L.720, H.723, L.724 Chain L: I.450, E.542, R.593, P.686, R.687, L.690 Ligands: MG.27 11 PLIP interactions: 9 interactions with chain I, 2 interactions with chain L Hydrogen bonds: I:Y.531, I:Y.531, I:S.573, I:S.573, I:K.574, I:S.575, I:S.575, I:Q.576 Salt bridges: I:K.574, L:R.687, L:R.687 ADP.23: 21 residues within 4Å: Chain G: H.531, I.533, R.676, V.807, R.808, E.811 Chain J: S.377, I.378, F.379, N.381, G.419, T.420, A.421, K.422, S.423, Q.424, I.568, H.571, V.572, I.575 Ligands: MG.24 13 PLIP interactions: 9 interactions with chain J, 4 interactions with chain G Hydrogen bonds: J:F.379, J:F.379, J:G.419, J:T.420, J:A.421, J:K.422, J:S.423, J:S.423, G:R.676, G:E.811 Salt bridges: J:K.422, G:R.808, G:R.808 ADP.28: 22 residues within 4Å: Chain H: L.434, E.526, Q.527, A.734, R.735, E.738 Chain L: E.421, I.422, Y.423, N.425, D.461, P.462, G.463, V.464, A.465, K.466, S.467, Q.468, L.612, H.615, V.616 Ligands: MG.29 15 PLIP interactions: 11 interactions with chain L, 4 interactions with chain H Hydrogen bonds: L:Y.423, L:Y.423, L:D.461, L:G.463, L:V.464, L:A.465, L:K.466, L:S.467, L:S.467, L:Q.468, H:Q.527, H:E.738 Salt bridges: L:K.466, H:R.735, H:R.735

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Greiwe, J.F. et al., Structural mechanism for the selective phosphorylation of DNA-loaded MCM double hexamers by the Dbf4-dependent kinase. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-02-02

Peptides

DNA replication licensing factor MCM2: AG
DNA replication licensing factor MCM3: BH
DNA replication licensing factor MCM4: CI
Minichromosome maintenance protein 5: DJ
DNA replication licensing factor MCM6: EK
DNA replication licensing factor MCM7: FL
Cell division control protein 7: M
DDK kinase regulatory subunit DBF4: N

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

M
1

N
G

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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