SMTL ID : 6mii.1

Crystal structure of minichromosome maintenance protein MCM/DNA complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

homo-hexamer

Ligands

3 x 08T: [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium(Non-covalent)

08T.1: 21 residues within 4Å: Chain A: S.300, I.301, Y.302, D.339, P.340, G.341, T.342, A.343, K.344, S.345, Q.346, E.403, N.446, I.493 Chain B: E.420, Q.421, R.471, P.557, R.558, E.561 Ligands: MG.3 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Y.302, A:Y.302, A:G.341, A:T.342, A:A.343, A:K.344, A:S.345, A:Q.346, B:E.420, B:Q.421 Water bridges: A:S.345, A:S.345, B:R.558 Salt bridges: A:K.344, B:R.558, B:R.558 08T.4: 22 residues within 4Å: Chain B: S.300, I.301, Y.302, H.304, P.340, G.341, T.342, A.343, K.344, S.345, Q.346, E.403, N.446, I.493 Chain C: I.328, E.420, Q.421, R.471, P.557, R.558, E.561 Ligands: MG.6 15 PLIP interactions: 5 interactions with chain C, 10 interactions with chain B Hydrogen bonds: C:Q.421, B:Y.302, B:Y.302, B:G.341, B:T.342, B:A.343, B:K.344, B:S.345, B:Q.346 Water bridges: C:R.558, C:R.558, B:S.345 Salt bridges: C:R.558, C:R.558, B:K.344 08T.7: 20 residues within 4Å: Chain C: S.300, I.301, Y.302, P.340, G.341, T.342, A.343, K.344, S.345, Q.346, E.403, N.446, I.493 Chain D: E.420, Q.421, R.471, P.557, R.558, E.561 Ligands: MG.9 14 PLIP interactions: 9 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:Y.302, C:Y.302, C:G.341, C:T.342, C:A.343, C:K.344, C:S.345, C:Q.346, D:Q.421 Salt bridges: C:K.344, D:R.558, D:R.558 Water bridges: D:R.558, D:R.558

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.145, C.150, C.172, C.175 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.145, A:C.150, A:C.172, A:C.175 ZN.5: 4 residues within 4Å: Chain B: H.145, C.150, C.172, C.175 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.145, B:C.150, B:C.172, B:C.175 ZN.8: 4 residues within 4Å: Chain C: H.145, C.150, C.172, C.175 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.145, C:C.150, C:C.172, C:C.175 ZN.11: 4 residues within 4Å: Chain D: H.145, C.150, C.172, C.175 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.145, D:C.150, D:C.172, D:C.175 ZN.14: 4 residues within 4Å: Chain E: H.145, C.150, C.172, C.175 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.145, E:C.150, E:C.172, E:C.175 ZN.17: 4 residues within 4Å: Chain F: H.145, C.150, C.172, C.175 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.145, F:C.150, F:C.172, F:C.175

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: S.345, D.402 Ligands: 08T.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.345, H2O.1, H2O.1, H2O.1 MG.6: 4 residues within 4Å: Chain B: S.345, D.402 Chain C: Q.421 Ligands: 08T.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.345, H2O.1, H2O.1, H2O.1 MG.9: 3 residues within 4Å: Chain C: S.345, D.402 Ligands: 08T.7 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:S.345, H2O.1, H2O.1, H2O.1 MG.12: 4 residues within 4Å: Chain D: S.345, D.402 Chain E: Q.421 Ligands: ADP.10 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:S.345, H2O.1, H2O.1, H2O.1 MG.15: 3 residues within 4Å: Chain E: S.345, D.402 Ligands: ADP.13 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:S.345, H2O.1, H2O.1, H2O.1 MG.18: 3 residues within 4Å: Chain F: S.345, D.402 Ligands: ADP.16 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:S.345, H2O.1, H2O.1, H2O.1

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

ADP.10: 18 residues within 4Å: Chain D: S.300, I.301, Y.302, H.304, D.339, G.341, T.342, A.343, K.344, S.345, Q.346, I.493 Chain E: E.420, Q.421, P.557, R.558, E.561 Ligands: MG.12 22 PLIP interactions: 13 interactions with chain D, 9 interactions with chain E Hydrogen bonds: D:Y.302, D:Y.302, D:D.339, D:G.341, D:T.342, D:A.343, D:K.344, D:S.345, D:Q.346, E:E.420, E:E.420, E:Q.421, E:E.561 Water bridges: D:S.345, D:D.402, D:D.402, E:Q.421, E:R.558, E:R.558 Salt bridges: D:K.344, E:R.558, E:R.558 ADP.13: 19 residues within 4Å: Chain E: S.300, I.301, Y.302, H.304, D.339, G.341, T.342, A.343, K.344, S.345, Q.346, I.493 Chain F: E.420, Q.421, R.471, P.557, R.558, E.561 Ligands: MG.15 21 PLIP interactions: 6 interactions with chain F, 15 interactions with chain E Hydrogen bonds: F:E.420, F:Q.421, F:E.561, E:Y.302, E:Y.302, E:G.341, E:T.342, E:A.343, E:K.344, E:S.345, E:Q.346, E:Q.346 Water bridges: F:R.558, E:S.345, E:S.345, E:S.345, E:D.402, E:E.403 Salt bridges: F:R.558, F:R.558, E:K.344 ADP.16: 16 residues within 4Å: Chain A: P.557, R.558, E.561 Chain F: S.300, I.301, Y.302, H.304, P.340, G.341, T.342, A.343, K.344, S.345, Q.346, I.493 Ligands: MG.18 17 PLIP interactions: 14 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:Y.302, F:Y.302, F:G.341, F:T.342, F:A.343, F:K.344, F:S.345, F:Q.346 Water bridges: F:K.344, F:K.344, F:S.345, F:S.345, F:S.345, A:R.558 Salt bridges: F:K.344, A:R.558, A:R.558

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meagher, M. et al., DNA translocation mechanism of the MCM complex and implications for replication initiation. Nat Commun (2019)

Release Date

2019-07-24

Peptides

Minichromosome maintenance protein MCM: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Minichromosome maintenance protein MCM

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