SMTL ID : 6h73.1

Molybdenum storage protein - recombinantly produced and loaded with molybdate under in vitro conditions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-3-3-mer

Ligands

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

ATP.1: 21 residues within 4Å: Chain A: K.41, G.43, G.44, Q.45, S.46, G.76, A.77, G.78, T.168, K.188, D.189, E.190, G.192, L.193, Y.194, A.196, N.197, P.198, K.199, S.223, I.224 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.44, A:Q.45, A:Q.45, A:S.46, A:A.77, A:D.189, A:E.190, A:E.190, A:Y.194, A:Y.194, A:N.197, A:S.223 Salt bridges: A:K.41, A:K.41, A:K.188, A:K.188, A:K.188 ATP.5: 22 residues within 4Å: Chain B: K.44, G.46, G.47, R.48, G.78, A.79, G.80, R.84, E.189, N.190, V.191, G.193, I.194, Y.195, A.197, D.198, P.199, N.200, P.224, L.225, P.226 Ligands: MG.6 20 PLIP interactions: 2 interactions with chain A, 18 interactions with chain B Water bridges: A:S.15, A:L.16, B:R.84, B:D.170, B:D.170 Hydrogen bonds: B:G.46, B:G.47, B:R.48, B:V.49, B:A.79, B:G.80, B:R.84, B:N.190, B:N.190, B:Y.195, B:Y.195, B:N.200, B:N.200 Salt bridges: B:K.44, B:K.44 ATP.11: 21 residues within 4Å: Chain C: K.41, G.43, G.44, Q.45, S.46, G.76, A.77, G.78, T.168, K.188, D.189, E.190, G.192, L.193, Y.194, A.196, N.197, P.198, K.199, S.223, I.224 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:G.44, C:Q.45, C:Q.45, C:S.46, C:A.77, C:D.189, C:E.190, C:E.190, C:Y.194, C:Y.194, C:N.197, C:S.223 Salt bridges: C:K.41, C:K.41, C:K.188, C:K.188, C:K.188 ATP.15: 22 residues within 4Å: Chain D: K.44, G.46, G.47, R.48, G.78, A.79, G.80, R.84, E.189, N.190, V.191, G.193, I.194, Y.195, A.197, D.198, P.199, N.200, P.224, L.225, P.226 Ligands: MG.16 21 PLIP interactions: 19 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.46, D:G.47, D:R.48, D:V.49, D:A.79, D:G.80, D:R.84, D:N.190, D:N.190, D:Y.195, D:Y.195, D:N.200, D:N.200 Water bridges: D:R.84, D:D.170, D:D.170, D:P.226, C:S.15, C:L.16 Salt bridges: D:K.44, D:K.44 ATP.21: 21 residues within 4Å: Chain E: K.41, G.43, G.44, Q.45, S.46, G.76, A.77, G.78, T.168, K.188, D.189, E.190, G.192, L.193, Y.194, A.196, N.197, P.198, K.199, S.223, I.224 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:G.44, E:Q.45, E:Q.45, E:S.46, E:A.77, E:D.189, E:E.190, E:E.190, E:Y.194, E:Y.194, E:N.197, E:S.223 Salt bridges: E:K.41, E:K.41, E:K.188, E:K.188, E:K.188 ATP.25: 22 residues within 4Å: Chain F: K.44, G.46, G.47, R.48, G.78, A.79, G.80, R.84, E.189, N.190, V.191, G.193, I.194, Y.195, A.197, D.198, P.199, N.200, P.224, L.225, P.226 Ligands: MG.26 20 PLIP interactions: 18 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:G.46, F:G.47, F:R.48, F:V.49, F:A.79, F:G.80, F:R.84, F:N.190, F:N.190, F:Y.195, F:Y.195, F:N.200, F:N.200 Water bridges: F:R.84, F:D.170, F:D.170, E:S.15, E:L.16 Salt bridges: F:K.44, F:K.44

12 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 4 residues within 4Å: Chain A: V.63, R.66, K.67, H.120 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.66, A:K.119 Salt bridges: A:R.66, A:K.67, A:H.120 PO4.3: 3 residues within 4Å: Chain A: R.209, E.241, H.261 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.209, A:H.261 PO4.9: 6 residues within 4Å: Chain A: P.150 Chain B: Y.154, H.155, H.156, H.157 Ligands: FUQ.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.156, B:H.157 Salt bridges: B:H.157 PO4.10: 4 residues within 4Å: Chain A: R.156 Chain B: F.159, H.167, D.233 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.156, B:H.167 PO4.12: 4 residues within 4Å: Chain C: V.63, R.66, K.67, H.120 5 PLIP interactions: 5 interactions with chain C Water bridges: C:R.66, C:K.119 Salt bridges: C:R.66, C:K.67, C:H.120 PO4.13: 3 residues within 4Å: Chain C: R.209, E.241, H.261 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.209, C:H.261 PO4.19: 6 residues within 4Å: Chain C: P.150 Chain D: Y.154, H.155, H.156, H.157 Ligands: FUQ.14 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.156, D:H.157 Salt bridges: D:H.157 PO4.20: 4 residues within 4Å: Chain C: R.156 Chain D: F.159, H.167, D.233 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Salt bridges: C:R.156, D:H.167 PO4.22: 4 residues within 4Å: Chain E: V.63, R.66, K.67, H.120 5 PLIP interactions: 5 interactions with chain E Water bridges: E:R.66, E:K.119 Salt bridges: E:R.66, E:K.67, E:H.120 PO4.23: 3 residues within 4Å: Chain E: R.209, E.241, H.261 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:R.209, E:H.261 PO4.29: 6 residues within 4Å: Chain E: P.150 Chain F: Y.154, H.155, H.156, H.157 Ligands: FUQ.24 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:H.156, F:H.157 Salt bridges: F:H.157 PO4.30: 4 residues within 4Å: Chain E: R.156 Chain F: F.159, H.167, D.233 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Salt bridges: F:H.167, E:R.156

3 x FUQ: Mo5 Cluster(Non-covalent)

FUQ.4: 12 residues within 4Å: Chain A: A.128, G.129, L.130 Chain B: P.102, H.155, H.156 Chain E: A.111, Q.115, V.124, G.126 Ligands: GUH.7, PO4.9 9 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A, 4 interactions with chain E Hydrogen bonds: B:H.155, B:H.156, A:G.129, A:L.130, A:L.130, E:Q.115, E:G.126, E:G.126 Water bridges: E:Q.115 FUQ.14: 12 residues within 4Å: Chain A: A.111, Q.115, V.124, G.126 Chain C: A.128, G.129, L.130 Chain D: P.102, H.155, H.156 Ligands: GUH.17, PO4.19 9 PLIP interactions: 3 interactions with chain C, 4 interactions with chain A, 2 interactions with chain D Hydrogen bonds: C:G.129, C:L.130, C:L.130, A:Q.115, A:G.126, A:G.126, D:H.155, D:H.156 Water bridges: A:Q.115 FUQ.24: 12 residues within 4Å: Chain C: A.111, Q.115, V.124, G.126 Chain E: A.128, G.129, L.130 Chain F: P.102, H.155, H.156 Ligands: GUH.27, PO4.29 9 PLIP interactions: 4 interactions with chain C, 3 interactions with chain E, 2 interactions with chain F Hydrogen bonds: C:Q.115, C:G.126, C:G.126, E:G.129, E:L.130, E:L.130, F:H.155, F:H.156 Water bridges: C:Q.115

3 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain B: D.170, E.189, P.226 Ligands: ATP.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.189, B:P.226, H2O.3, H2O.3 MG.16: 4 residues within 4Å: Chain D: D.170, E.189, P.226 Ligands: ATP.15 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.189, D:P.226, H2O.6, H2O.6 MG.26: 4 residues within 4Å: Chain F: D.170, E.189, P.226 Ligands: ATP.25 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.189, F:P.226, H2O.9, H2O.9

3 x GUH: Mo6 cluster(Non-covalent)

GUH.7: 12 residues within 4Å: Chain B: A.105, S.106, G.109, Q.110, H.113, Y.126, E.128, H.129, P.130, S.149, H.155 Ligands: FUQ.4 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.106, B:G.109, B:Q.110, B:H.113, B:H.113, B:Y.126, B:Y.126, B:E.128, B:H.129, B:S.149 Water bridges: B:H.129 GUH.17: 12 residues within 4Å: Chain D: A.105, S.106, G.109, Q.110, H.113, Y.126, E.128, H.129, P.130, S.149, H.155 Ligands: FUQ.14 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:S.106, D:G.109, D:Q.110, D:H.113, D:H.113, D:Y.126, D:Y.126, D:E.128, D:H.129, D:S.149 Water bridges: D:H.129 GUH.27: 12 residues within 4Å: Chain F: A.105, S.106, G.109, Q.110, H.113, Y.126, E.128, H.129, P.130, S.149, H.155 Ligands: FUQ.24 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:S.106, F:G.109, F:Q.110, F:H.113, F:H.113, F:Y.126, F:Y.126, F:E.128, F:H.129, F:S.149 Water bridges: F:H.129

3 x MOO: MOLYBDATE ION(Non-covalent)

MOO.8: 6 residues within 4Å: Chain B: H.139 Chain D: H.139 Chain F: Q.135, H.139 Ligands: MOO.18, MOO.28 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.139 MOO.18: 6 residues within 4Å: Chain B: Q.135, H.139 Chain D: H.139 Chain F: H.139 Ligands: MOO.8, MOO.28 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:H.139 MOO.28: 6 residues within 4Å: Chain B: H.139 Chain D: Q.135, H.139 Chain F: H.139 Ligands: MOO.8, MOO.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brunle, S. et al., The molybdenum storage protein - A bionanolab for creating experimentally alterable polyoxomolybdate clusters. J. Inorg. Biochem. (2018)

Release Date

2018-11-14

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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