SMTL ID : 4r7y.1

Crystal structure of an active MCM hexamer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-hexamer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: A.303, I.304, Y.305, Y.307, P.344, G.345, V.346, A.347, K.348, S.349, Q.350, N.450, V.494, H.497, I.498 Chain B: A.569, E.573 Ligands: MG.2 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.305, A:Y.305, A:G.345, A:V.346, A:A.347, A:K.348, A:S.349, A:S.349, A:Q.350, B:E.573 Salt bridges: A:K.348 ADP.7: 19 residues within 4Å: Chain B: A.303, I.304, Y.305, Y.307, D.343, P.344, G.345, V.346, A.347, K.348, S.349, Q.350, N.450, V.494, H.497, I.498 Chain E: A.569, E.573 Ligands: MG.8 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:Y.305, B:Y.305, B:G.345, B:A.347, B:K.348, B:S.349, B:S.349, B:Q.350, E:E.573, E:E.573 Salt bridges: B:K.348 ADP.13: 18 residues within 4Å: Chain C: A.303, I.304, Y.305, Y.307, P.344, G.345, V.346, A.347, K.348, S.349, Q.350, N.450, V.494, H.497, I.498 Chain D: A.569, E.573 Ligands: MG.14 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Y.305, C:Y.305, C:G.345, C:V.346, C:A.347, C:K.348, C:S.349, C:S.349, C:Q.350, D:E.573 Salt bridges: C:K.348 ADP.19: 19 residues within 4Å: Chain A: A.569, E.573 Chain D: A.303, I.304, Y.305, Y.307, D.343, P.344, G.345, V.346, A.347, K.348, S.349, Q.350, N.450, V.494, H.497, I.498 Ligands: MG.20 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain D Hydrogen bonds: A:E.573, A:E.573, D:Y.305, D:Y.305, D:G.345, D:A.347, D:K.348, D:S.349, D:S.349, D:Q.350 Salt bridges: D:K.348 ADP.25: 18 residues within 4Å: Chain E: A.303, I.304, Y.305, Y.307, P.344, G.345, V.346, A.347, K.348, S.349, Q.350, N.450, V.494, H.497, I.498 Chain F: A.569, E.573 Ligands: MG.26 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:Y.305, E:Y.305, E:G.345, E:V.346, E:A.347, E:K.348, E:S.349, E:S.349, E:Q.350, F:E.573 Salt bridges: E:K.348 ADP.31: 19 residues within 4Å: Chain C: A.569, E.573 Chain F: A.303, I.304, Y.305, Y.307, D.343, P.344, G.345, V.346, A.347, K.348, S.349, Q.350, N.450, V.494, H.497, I.498 Ligands: MG.32 11 PLIP interactions: 2 interactions with chain C, 9 interactions with chain F Hydrogen bonds: C:E.573, C:E.573, F:Y.305, F:Y.305, F:G.345, F:A.347, F:K.348, F:S.349, F:S.349, F:Q.350 Salt bridges: F:K.348

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.349 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.349 MG.8: 3 residues within 4Å: Chain B: S.349, D.406 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.349 MG.14: 2 residues within 4Å: Chain C: S.349 Ligands: ADP.13 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.349 MG.20: 3 residues within 4Å: Chain D: S.349, D.406 Ligands: ADP.19 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.349 MG.26: 2 residues within 4Å: Chain E: S.349 Ligands: ADP.25 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.349 MG.32: 3 residues within 4Å: Chain F: S.349, D.406 Ligands: ADP.31 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.349

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 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.9: 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.15: 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.21: 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.27: 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.33: 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

18 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 1 residues within 4Å: Chain A: V.107 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: R.231, K.268, L.439, N.440 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: R.106, K.120 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain B: V.107 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: R.231, K.268, L.439, N.440 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: R.106, K.120 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain C: V.107 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain C: R.231, K.268, L.439, N.440 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain C: R.106, K.120 Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain D: V.107 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain D: R.231, K.268, L.439, N.440 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain D: R.106, K.120 Ligand excluded by PLIP CL.28: 1 residues within 4Å: Chain E: V.107 Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain E: R.231, K.268, L.439, N.440 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain E: R.106, K.120 Ligand excluded by PLIP CL.34: 1 residues within 4Å: Chain F: V.107 Ligand excluded by PLIP CL.35: 4 residues within 4Å: Chain F: R.231, K.268, L.439, N.440 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain F: R.106, K.120 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller, J.M. et al., Analysis of the crystal structure of an active MCM hexamer. Elife (2014)

Release Date

2014-10-08

Peptides

Minichromosome maintenance protein MCM, Cell division control protein 21: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Minichromosome maintenance protein MCM, Cell division control protein 21