SMTL ID : 6sko.1

Cryo-EM Structure of the Fork Protection Complex Bound to CMG at a Replication Fork - conformation 2 MCM CTD:ssDNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

5 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 23 residues within 4Å: Chain A: 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, H.730, I.731, H.735 Chain F: Y.558, E.650, R.701, T.795, R.796, E.799 Ligands: MG.2 19 PLIP interactions: 12 interactions with chain A, 7 interactions with chain F Hydrogen bonds: A:F.538, A:H.540, A:S.578, A:T.579, A:T.579, A:S.580, A:S.580, A:K.581, A:K.581, A:S.582, A:Q.583, A:N.683, F:R.701, F:R.701, F:R.796, F:R.796, F:E.799, F:E.799 Salt bridges: F:R.796 ANP.3: 22 residues within 4Å: Chain B: E.421, I.422, Y.423, N.425, D.461, P.462, G.463, V.464, A.465, K.466, S.467, Q.468, N.568, L.612, V.616 Chain E: E.491, S.538, R.542, A.699, R.700, E.703 Ligands: MG.4 16 PLIP interactions: 10 interactions with chain B, 6 interactions with chain E Hydrogen bonds: B:Y.423, B:Y.423, B:G.463, B:V.464, B:A.465, B:K.466, B:K.466, B:S.467, B:Q.468, B:N.568, E:R.542, E:R.542, E:R.700, E:R.700, E:E.703 Salt bridges: E:R.700 ANP.5: 23 residues within 4Å: Chain A: E.657, Q.658, P.704, R.708, V.797, R.798, E.801 Chain C: S.504, 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 Ligands: MG.6 21 PLIP interactions: 13 interactions with chain C, 8 interactions with chain A Hydrogen bonds: C:Y.506, C:Y.506, C:G.546, C:T.547, C:A.548, C:K.549, C:K.549, C:S.550, C:S.550, C:S.550, C:Q.551, C:Q.551, A:Q.658, A:R.708, A:R.708, A:R.798, A:R.798, A:E.801, A:E.801 Salt bridges: C:K.549, A:R.798 ANP.7: 22 residues within 4Å: Chain D: S.548, R.549, I.650, R.651, E.654, R.658 Chain E: S.370, I.371, Y.372, D.410, P.411, S.412, T.413, A.414, K.415, S.416, Q.417, N.517, I.561, H.564, V.565 Ligands: MG.8 18 PLIP interactions: 11 interactions with chain E, 7 interactions with chain D Hydrogen bonds: E:Y.372, E:S.412, E:T.413, E:T.413, E:A.414, E:K.415, E:K.415, E:S.416, E:Q.417, E:N.517, D:R.549, D:R.549, D:R.651, D:R.651, D:R.651, D:E.654 Salt bridges: E:K.415, D:R.651 ANP.9: 25 residues within 4Å: Chain B: M.448, I.450, E.542, A.589, R.593, P.686, R.687, L.690 Chain F: S.529, I.530, Y.531, L.533, D.569, P.570, S.571, T.572, S.573, K.574, S.575, Q.576, N.676, L.720, H.723, L.724 Ligands: MG.10 16 PLIP interactions: 9 interactions with chain F, 7 interactions with chain B Hydrogen bonds: F:Y.531, F:Y.531, F:S.571, F:T.572, F:S.573, F:K.574, F:K.574, F:S.575, F:Q.576, B:E.542, B:E.542, B:R.593, B:R.593, B:R.687, B:R.687 Salt bridges: B:R.687

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: K.581, S.582 Chain F: E.650, R.701, R.796 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.582 MG.4: 4 residues within 4Å: Chain B: K.466, S.467 Chain E: R.542 Ligands: ANP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.467 MG.6: 4 residues within 4Å: Chain C: K.549, S.550, A.649 Ligands: ANP.5 No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Chain D: R.549, R.651 Chain E: K.415, S.416 Ligands: ANP.7 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain B: R.593, R.687 Chain F: S.575 Ligands: ANP.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baretic, D. et al., Cryo-EM Structure of the Fork Protection Complex Bound to CMG at a Replication Fork. Mol.Cell (2020)

Release Date

2020-05-06

Peptides

DNA replication licensing factor MCM6: A
DNA replication licensing factor MCM7: B
DNA replication licensing factor MCM2: C
Minichromosome maintenance protein 5: D
DNA replication licensing factor MCM3: E
DNA replication licensing factor MCM4: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
6

B
7

C
2

D
5

E
3

F
4

DNA replication licensing factor MCM6

DNA replication licensing factor MCM7

DNA replication licensing factor MCM2

Minichromosome maintenance protein 5

DNA replication licensing factor MCM3

DNA replication licensing factor MCM4

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