SMTL ID : 4ndq.1

Crystal structure Molybdenum Storage Protein with fully Mo-loaded cavity

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-3-3-mer

Ligands

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

ATP.1: 22 residues within 4Å: Chain A: K.42, G.44, G.45, Q.46, S.47, G.77, A.78, G.79, T.169, D.170, K.189, D.190, E.191, G.193, L.194, Y.195, A.197, N.198, P.199, K.200, S.224, I.225 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:G.45, A:Q.46, A:S.47, A:S.47, A:A.78, A:T.169, A:D.190, A:Y.195, A:Y.195, A:N.198, A:K.200, A:K.200, A:S.224 Water bridges: A:K.42, A:K.42, A:G.79, A:G.79, A:G.79, A:G.79, A:N.198, A:N.198 Salt bridges: A:K.42, A:K.42, A:K.189, A:K.189 ATP.6: 22 residues within 4Å: Chain B: K.45, G.47, G.48, R.49, G.79, A.80, G.81, R.85, E.190, N.191, V.192, G.194, I.195, Y.196, A.198, D.199, P.200, N.201, P.225, L.226, P.227 Ligands: MG.7 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.48, B:R.49, B:A.80, B:G.81, B:R.85, B:N.191, B:N.191, B:Y.196, B:Y.196, B:N.201, B:P.227 Water bridges: B:R.49, B:D.171, A:S.16 Salt bridges: B:K.45, B:K.45, B:R.49 ATP.13: 22 residues within 4Å: Chain C: K.42, G.44, G.45, Q.46, S.47, G.77, A.78, G.79, T.169, D.170, K.189, D.190, E.191, G.193, L.194, Y.195, A.197, N.198, P.199, K.200, S.224, I.225 25 PLIP interactions: 25 interactions with chain C Hydrogen bonds: C:G.45, C:Q.46, C:S.47, C:S.47, C:A.78, C:T.169, C:D.190, C:Y.195, C:Y.195, C:N.198, C:K.200, C:K.200, C:S.224 Water bridges: C:K.42, C:K.42, C:G.79, C:G.79, C:G.79, C:G.79, C:N.198, C:N.198 Salt bridges: C:K.42, C:K.42, C:K.189, C:K.189 ATP.18: 22 residues within 4Å: Chain D: K.45, G.47, G.48, R.49, G.79, A.80, G.81, R.85, E.190, N.191, V.192, G.194, I.195, Y.196, A.198, D.199, P.200, N.201, P.225, L.226, P.227 Ligands: MG.19 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.48, D:R.49, D:A.80, D:G.81, D:R.85, D:N.191, D:N.191, D:Y.196, D:Y.196, D:N.201, D:P.227 Water bridges: D:R.49, D:D.171, C:S.16 Salt bridges: D:K.45, D:K.45, D:R.49 ATP.25: 22 residues within 4Å: Chain E: K.42, G.44, G.45, Q.46, S.47, G.77, A.78, G.79, T.169, D.170, K.189, D.190, E.191, G.193, L.194, Y.195, A.197, N.198, P.199, K.200, S.224, I.225 25 PLIP interactions: 25 interactions with chain E Hydrogen bonds: E:G.45, E:Q.46, E:S.47, E:S.47, E:A.78, E:T.169, E:D.190, E:Y.195, E:Y.195, E:N.198, E:K.200, E:K.200, E:S.224 Water bridges: E:K.42, E:K.42, E:G.79, E:G.79, E:G.79, E:G.79, E:N.198, E:N.198 Salt bridges: E:K.42, E:K.42, E:K.189, E:K.189 ATP.30: 22 residues within 4Å: Chain F: K.45, G.47, G.48, R.49, G.79, A.80, G.81, R.85, E.190, N.191, V.192, G.194, I.195, Y.196, A.198, D.199, P.200, N.201, P.225, L.226, P.227 Ligands: MG.31 17 PLIP interactions: 16 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.48, F:R.49, F:A.80, F:G.81, F:R.85, F:N.191, F:N.191, F:Y.196, F:Y.196, F:N.201, F:P.227 Water bridges: F:R.49, F:D.171, E:S.16 Salt bridges: F:K.45, F:K.45, F:R.49

6 x 8M0: bis(mu4-oxo)-tetrakis(mu3-oxo)-hexakis(mu2-oxo)-hexadecaoxo-octamolybdenum (VI)(Non-covalent)

8M0.2: 17 residues within 4Å: Chain A: V.126, G.127, G.128, G.130, L.131, F.146, S.147, M.149, P.150, P.151, L.176, F.180 Chain B: Y.155, H.156, H.157, H.158 Ligands: 8M0.8 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.130, A:M.149, B:H.156, B:H.157, B:H.158, B:H.158 8M0.8: 16 residues within 4Å: Chain B: P.103, A.106, S.107, G.110, Q.111, H.114, Y.127, E.129, H.130, P.131, S.150, F.152, P.153, P.154, H.156 Ligands: 8M0.2 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:A.106, B:Q.111, B:Y.127, B:H.130, B:H.130, B:H.130, B:S.150, B:H.156 8M0.14: 17 residues within 4Å: Chain C: V.126, G.127, G.128, G.130, L.131, F.146, S.147, M.149, P.150, P.151, L.176, F.180 Chain D: Y.155, H.156, H.157, H.158 Ligands: 8M0.20 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:H.156, D:H.157, D:H.158, D:H.158, C:G.130, C:M.149 8M0.20: 16 residues within 4Å: Chain D: P.103, A.106, S.107, G.110, Q.111, H.114, Y.127, E.129, H.130, P.131, S.150, F.152, P.153, P.154, H.156 Ligands: 8M0.14 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:A.106, D:Q.111, D:Y.127, D:H.130, D:H.130, D:H.130, D:S.150, D:H.156 8M0.26: 17 residues within 4Å: Chain E: V.126, G.127, G.128, G.130, L.131, F.146, S.147, M.149, P.150, P.151, L.176, F.180 Chain F: Y.155, H.156, H.157, H.158 Ligands: 8M0.32 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:G.130, E:M.149, F:H.156, F:H.157, F:H.158, F:H.158 8M0.32: 16 residues within 4Å: Chain F: P.103, A.106, S.107, G.110, Q.111, H.114, Y.127, E.129, H.130, P.131, S.150, F.152, P.153, P.154, H.156 Ligands: 8M0.26 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:A.106, F:Q.111, F:Y.127, F:H.130, F:H.130, F:H.130, F:S.150, F:H.156

18 x MO: MOLYBDENUM ATOM(Non-covalent)(Non-functional Binders)

MO.3: 9 residues within 4Å: Chain A: A.133, S.137 Chain C: L.136 Ligands: MO.4, MO.5, MO.16, MO.17, MO.28, MO.29 Ligand excluded by PLIP MO.4: 11 residues within 4Å: Chain A: L.136 Chain C: L.136 Chain E: L.136 Ligands: MO.3, MO.5, MO.15, MO.16, MO.17, MO.27, MO.28, MO.29 Ligand excluded by PLIP MO.5: 8 residues within 4Å: Ligands: MO.3, MO.4, MO.15, MO.16, MO.17, MO.27, MO.28, MO.29 Ligand excluded by PLIP MO.10: 6 residues within 4Å: Chain B: T.132 Ligands: MO.11, MO.12, MO.23, MO.24, MO.36 Ligand excluded by PLIP MO.11: 5 residues within 4Å: Ligands: MO.10, MO.12, MO.24, MO.34, MO.36 Ligand excluded by PLIP MO.12: 8 residues within 4Å: Ligands: MO.10, MO.11, MO.22, MO.23, MO.24, MO.34, MO.35, MO.36 Ligand excluded by PLIP MO.15: 9 residues within 4Å: Chain C: A.133, S.137 Chain E: L.136 Ligands: MO.4, MO.5, MO.16, MO.17, MO.28, MO.29 Ligand excluded by PLIP MO.16: 11 residues within 4Å: Chain A: L.136 Chain C: L.136 Chain E: L.136 Ligands: MO.3, MO.4, MO.5, MO.15, MO.17, MO.27, MO.28, MO.29 Ligand excluded by PLIP MO.17: 8 residues within 4Å: Ligands: MO.3, MO.4, MO.5, MO.15, MO.16, MO.27, MO.28, MO.29 Ligand excluded by PLIP MO.22: 6 residues within 4Å: Chain D: T.132 Ligands: MO.12, MO.23, MO.24, MO.35, MO.36 Ligand excluded by PLIP MO.23: 5 residues within 4Å: Ligands: MO.10, MO.12, MO.22, MO.24, MO.36 Ligand excluded by PLIP MO.24: 8 residues within 4Å: Ligands: MO.10, MO.11, MO.12, MO.22, MO.23, MO.34, MO.35, MO.36 Ligand excluded by PLIP MO.27: 9 residues within 4Å: Chain A: L.136 Chain E: A.133, S.137 Ligands: MO.4, MO.5, MO.16, MO.17, MO.28, MO.29 Ligand excluded by PLIP MO.28: 11 residues within 4Å: Chain A: L.136 Chain C: L.136 Chain E: L.136 Ligands: MO.3, MO.4, MO.5, MO.15, MO.16, MO.17, MO.27, MO.29 Ligand excluded by PLIP MO.29: 8 residues within 4Å: Ligands: MO.3, MO.4, MO.5, MO.15, MO.16, MO.17, MO.27, MO.28 Ligand excluded by PLIP MO.34: 6 residues within 4Å: Chain F: T.132 Ligands: MO.11, MO.12, MO.24, MO.35, MO.36 Ligand excluded by PLIP MO.35: 5 residues within 4Å: Ligands: MO.12, MO.22, MO.24, MO.34, MO.36 Ligand excluded by PLIP MO.36: 8 residues within 4Å: Ligands: MO.10, MO.11, MO.12, MO.22, MO.23, MO.24, MO.34, MO.35 Ligand excluded by PLIP

3 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 5 residues within 4Å: Chain B: K.45, D.171, P.227, V.228 Ligands: ATP.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.171, B:P.227 MG.19: 5 residues within 4Å: Chain D: K.45, D.171, P.227, V.228 Ligands: ATP.18 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.171, D:P.227 MG.31: 5 residues within 4Å: Chain F: K.45, D.171, P.227, V.228 Ligands: ATP.30 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.171, F:P.227

3 x M10: (mu3-oxo)-tris(mu2-oxo)-nonakisoxo-trimolybdenum (VI)(Non-covalent)

M10.9: 9 residues within 4Å: Chain B: T.132, Q.136, H.140 Chain D: H.140 Chain F: Q.136, I.139, H.140 Ligands: M10.21, M10.33 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Q.136, F:Q.136, F:H.140 M10.21: 9 residues within 4Å: Chain B: Q.136, I.139, H.140 Chain D: T.132, Q.136, H.140 Chain F: H.140 Ligands: M10.9, M10.33 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.136, B:Q.136, B:H.140 M10.33: 9 residues within 4Å: Chain B: H.140 Chain D: Q.136, I.139, H.140 Chain F: T.132, Q.136, H.140 Ligands: M10.9, M10.21 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.136, D:Q.136, D:H.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Poppe, J. et al., Structural diversity of polyoxomolybdate clusters along the three-fold axis of the molybdenum storage protein. J.Inorg.Biochem. (2014)

Release Date

2014-08-13

Peptides

Molybdenum storage protein subunit beta: ACE
Molybdenum storage protein subunit alpha: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
B

E
B

B
A

D
A

F
A

Molybdenum storage protein subunit beta

Molybdenum storage protein subunit alpha

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