SMTL ID : 6h74.1

The molybdenum storage protein - L131H

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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.41, G.43, G.44, Q.45, S.46, G.76, A.77, G.78, T.168, D.169, K.188, D.189, G.192, L.193, Y.194, A.196, N.197, P.198, K.199, L.220, S.223, I.224 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.44, A:Q.45, A:S.46, A:A.77, A:T.168, A:D.189, A:Y.194, A:Y.194, A:N.197, A:K.199, A:K.199 Water bridges: A:G.78, A:G.78, A:G.78, A:G.78 Salt bridges: A:K.41, A:K.41, A:K.188, A:K.188 ATP.7: 25 residues within 4Å: Chain A: S.15 Chain B: K.44, G.46, G.47, R.48, V.49, G.78, A.79, G.80, R.84, A.169, 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.8 19 PLIP interactions: 19 interactions with chain B 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 Water bridges: B:K.44, B:K.44, B:K.44, B:D.170 Salt bridges: B:K.44, B:K.44 ATP.11: 22 residues within 4Å: Chain C: K.41, G.43, G.44, Q.45, S.46, G.76, A.77, G.78, T.168, D.169, K.188, D.189, G.192, L.193, Y.194, A.196, N.197, P.198, K.199, L.220, S.223, I.224 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:G.44, C:Q.45, C:S.46, C:A.77, C:T.168, C:D.189, C:Y.194, C:Y.194, C:N.197, C:K.199, C:K.199 Water bridges: C:G.78, C:G.78, C:G.78, C:G.78 Salt bridges: C:K.41, C:K.41, C:K.188, C:K.188 ATP.17: 25 residues within 4Å: Chain C: S.15 Chain D: K.44, G.46, G.47, R.48, V.49, G.78, A.79, G.80, R.84, A.169, 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.18 19 PLIP interactions: 19 interactions with chain D 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:K.44, D:K.44, D:K.44, D:D.170 Salt bridges: D:K.44, D:K.44 ATP.21: 22 residues within 4Å: Chain E: K.41, G.43, G.44, Q.45, S.46, G.76, A.77, G.78, T.168, D.169, K.188, D.189, G.192, L.193, Y.194, A.196, N.197, P.198, K.199, L.220, S.223, I.224 19 PLIP interactions: 19 interactions with chain E Hydrogen bonds: E:G.44, E:Q.45, E:S.46, E:A.77, E:T.168, E:D.189, E:Y.194, E:Y.194, E:N.197, E:K.199, E:K.199 Water bridges: E:G.78, E:G.78, E:G.78, E:G.78 Salt bridges: E:K.41, E:K.41, E:K.188, E:K.188 ATP.27: 25 residues within 4Å: Chain E: S.15 Chain F: K.44, G.46, G.47, R.48, V.49, G.78, A.79, G.80, R.84, A.169, 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.28 19 PLIP interactions: 19 interactions with chain F 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:K.44, F:K.44, F:K.44, F:D.170 Salt bridges: F:K.44, F:K.44

6 x FUQ: Mo5 Cluster(Covalent)

FUQ.2: 8 residues within 4Å: Chain A: Q.100, S.103, S.104, D.107, K.152 Chain B: D.134 Chain D: E.128 Ligands: GWN.19 10 PLIP interactions: 2 interactions with chain D, 7 interactions with chain A, 1 interactions with chain B Water bridges: D:E.128, D:E.128, A:S.103, A:S.103, A:S.103, A:D.107 Hydrogen bonds: A:Q.100, A:S.103, A:K.152, B:D.134 FUQ.6: 11 residues within 4Å: Chain A: G.126, G.127, A.128, G.129, H.130, P.150 Chain B: P.102, Y.154, H.155, H.156, H.157 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.126, A:G.129, A:H.130, A:H.130, A:H.130, B:Y.154, B:H.156, B:H.156, B:H.157, B:H.157 Water bridges: A:A.128, A:A.128 FUQ.12: 8 residues within 4Å: Chain C: Q.100, S.103, S.104, D.107, K.152 Chain D: D.134 Chain F: E.128 Ligands: GWN.29 10 PLIP interactions: 7 interactions with chain C, 2 interactions with chain F, 1 interactions with chain D Hydrogen bonds: C:Q.100, C:S.103, C:K.152, D:D.134 Water bridges: C:S.103, C:S.103, C:S.103, C:D.107, F:E.128, F:E.128 FUQ.16: 11 residues within 4Å: Chain C: G.126, G.127, A.128, G.129, H.130, P.150 Chain D: P.102, Y.154, H.155, H.156, H.157 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:G.126, C:G.129, C:H.130, C:H.130, C:H.130, D:Y.154, D:H.156, D:H.157, D:H.157 Water bridges: C:A.128, C:A.128 FUQ.22: 8 residues within 4Å: Chain B: E.128 Chain E: Q.100, S.103, S.104, D.107, K.152 Chain F: D.134 Ligands: GWN.9 10 PLIP interactions: 7 interactions with chain E, 2 interactions with chain B, 1 interactions with chain F Hydrogen bonds: E:Q.100, E:S.103, E:K.152, F:D.134 Water bridges: E:S.103, E:S.103, E:S.103, E:D.107, B:E.128, B:E.128 FUQ.26: 11 residues within 4Å: Chain E: G.126, G.127, A.128, G.129, H.130, P.150 Chain F: P.102, Y.154, H.155, H.156, H.157 12 PLIP interactions: 7 interactions with chain E, 5 interactions with chain F Hydrogen bonds: E:G.126, E:G.129, E:H.130, E:H.130, E:H.130, F:Y.154, F:H.156, F:H.156, F:H.157, F:H.157 Water bridges: E:A.128, E:A.128

3 x GWW: pentakis(oxidanyl)molybdenum(Non-covalent)

GWW.3: 3 residues within 4Å: Chain A: H.130 Ligands: GWW.13, GWW.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.130 GWW.13: 3 residues within 4Å: Chain C: H.130 Ligands: GWW.3, GWW.23 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.130 GWW.23: 3 residues within 4Å: Chain E: H.130 Ligands: GWW.3, GWW.13 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.130

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

PO4.4: 3 residues within 4Å: Chain A: N.68, H.69, A.258 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.258 Salt bridges: A:H.69 PO4.5: 4 residues within 4Å: Chain A: R.209, E.241, H.261, I.265 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.209, A:H.261 PO4.14: 3 residues within 4Å: Chain C: N.68, H.69, A.258 2 PLIP interactions: 2 interactions with chain C Water bridges: C:A.258 Salt bridges: C:H.69 PO4.15: 4 residues within 4Å: Chain C: R.209, E.241, H.261, I.265 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.209, C:H.261 PO4.24: 3 residues within 4Å: Chain E: N.68, H.69, A.258 2 PLIP interactions: 2 interactions with chain E Water bridges: E:A.258 Salt bridges: E:H.69 PO4.25: 4 residues within 4Å: Chain E: R.209, E.241, H.261, I.265 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:R.209, E:H.261

3 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 5 residues within 4Å: Chain B: K.44, D.170, E.189, P.226 Ligands: ATP.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.189, B:P.226, H2O.9, H2O.9 MG.18: 5 residues within 4Å: Chain D: K.44, D.170, E.189, P.226 Ligands: ATP.17 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.189, D:P.226, H2O.23, H2O.23 MG.28: 5 residues within 4Å: Chain F: K.44, D.170, E.189, P.226 Ligands: ATP.27 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.189, F:P.226, H2O.38, H2O.38

3 x GWN: Mo8 cluster(Non-covalent)

GWN.9: 14 residues within 4Å: Chain B: P.102, A.105, S.106, G.109, Q.110, H.113, Y.126, E.128, H.129, P.130, S.149, P.153, H.155 Ligands: FUQ.22 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:A.105, B:S.106, B:Q.110, B:H.113, B:Y.126, B:V.127, B:E.128, B:H.129, B:S.149, B:H.155 GWN.19: 14 residues within 4Å: Chain D: P.102, A.105, S.106, G.109, Q.110, H.113, Y.126, E.128, H.129, P.130, S.149, P.153, H.155 Ligands: FUQ.2 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:A.105, D:S.106, D:Q.110, D:H.113, D:Y.126, D:V.127, D:E.128, D:H.129, D:S.149, D:H.155 GWN.29: 14 residues within 4Å: Chain F: P.102, A.105, S.106, G.109, Q.110, H.113, Y.126, E.128, H.129, P.130, S.149, P.153, H.155 Ligands: FUQ.12 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:A.105, F:S.106, F:Q.110, F:H.113, F:Y.126, F:V.127, F:E.128, F:H.129, F:S.149, F:H.155

3 x MOO: MOLYBDATE ION(Non-covalent)

MOO.10: 7 residues within 4Å: Chain B: T.131, H.139 Chain D: H.139 Chain F: I.138, H.139 Ligands: MOO.20, MOO.30 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.139 MOO.20: 7 residues within 4Å: Chain B: I.138, H.139 Chain D: T.131, H.139 Chain F: H.139 Ligands: MOO.10, MOO.30 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:H.139 MOO.30: 7 residues within 4Å: Chain B: H.139 Chain D: I.138, H.139 Chain F: T.131, H.139 Ligands: MOO.10, MOO.20 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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