SMTL ID : 7zqq.1

Molybdenum storage protein - LB131H

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-3-3-mer

Ligands

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

ATP.1: 23 residues within 4Å: Chain A: K.44, G.46, G.47, R.48, V.49, 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.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.47, A:R.48, A:V.49, A:A.79, A:G.80, A:R.84, A:N.190, A:N.190, A:Y.195, A:Y.195, A:N.200, A:N.200 Water bridges: A:K.44, A:K.44, A:K.44, A:R.52, A:R.84, A:D.170 Salt bridges: A:K.44, A:K.44 ATP.7: 21 residues within 4Å: Chain B: K.41, G.43, G.44, Q.45, S.46, G.76, A.77, G.78, T.168, 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 B Hydrogen bonds: B:G.44, B:Q.45, B:S.46, B:A.77, B:D.189, B:Y.194, B:Y.194, B:N.197, B:K.199, B:K.199 Water bridges: B:K.41, B:K.41, B:G.78, B:G.78, B:K.188 Salt bridges: B:K.41, B:K.41, B:K.188, B:K.188 ATP.14: 23 residues within 4Å: Chain C: K.44, G.46, G.47, R.48, V.49, 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.15 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:G.47, C:R.48, C:V.49, C:A.79, C:G.80, C:R.84, C:N.190, C:N.190, C:Y.195, C:Y.195, C:N.200, C:N.200 Water bridges: C:K.44, C:K.44, C:K.44, C:R.52, C:R.84, C:D.170 Salt bridges: C:K.44, C:K.44 ATP.20: 21 residues within 4Å: Chain D: K.41, G.43, G.44, Q.45, S.46, G.76, A.77, G.78, T.168, 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 D Hydrogen bonds: D:G.44, D:Q.45, D:S.46, D:A.77, D:D.189, D:Y.194, D:Y.194, D:N.197, D:K.199, D:K.199 Water bridges: D:K.41, D:K.41, D:G.78, D:G.78, D:K.188 Salt bridges: D:K.41, D:K.41, D:K.188, D:K.188 ATP.27: 23 residues within 4Å: Chain E: K.44, G.46, G.47, R.48, V.49, 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.28 23 PLIP interactions: 23 interactions with chain E Hydrogen bonds: E:G.47, E:R.48, E:V.49, E:A.79, E:G.80, E:R.84, E:N.190, E:N.190, E:Y.195, E:Y.195, E:N.200, E:N.200 Water bridges: E:K.44, E:K.44, E:K.44, E:R.52, E:R.84, E:D.170, E:D.170, E:E.189, E:E.189 Salt bridges: E:K.44, E:K.44 ATP.33: 21 residues within 4Å: Chain F: K.41, G.43, G.44, Q.45, S.46, G.76, A.77, G.78, T.168, 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 F Hydrogen bonds: F:G.44, F:Q.45, F:S.46, F:A.77, F:D.189, F:Y.194, F:Y.194, F:N.197, F:K.199, F:K.199 Water bridges: F:K.41, F:K.41, F:G.78, F:G.78, F:K.188 Salt bridges: F:K.41, F:K.41, F:K.188, F:K.188

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.170, E.189, P.226 Ligands: ATP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.189, A:P.226, H2O.1, H2O.1 MG.15: 4 residues within 4Å: Chain C: D.170, E.189, P.226 Ligands: ATP.14 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.189, C:P.226, H2O.13, H2O.14 MG.28: 4 residues within 4Å: Chain E: D.170, E.189, P.226 Ligands: ATP.27 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.189, E:P.226, H2O.26, H2O.26

18 x UNL: UNKNOWN LIGAND

UNL.3: 9 residues within 4Å: Chain A: T.131, H.139 Chain C: H.139 Chain E: T.131, Q.135, I.138, H.139 Ligands: UNL.16, UNL.29 Ligand excluded by PLIP UNL.4: 4 residues within 4Å: Chain A: E.128, P.130, T.131 Ligands: UNL.5 Ligand excluded by PLIP UNL.5: 20 residues within 4Å: Chain A: P.102, A.105, S.106, G.109, Q.110, H.113, Y.126, V.127, E.128, H.129, P.130, S.149, H.155 Chain E: D.134 Chain F: S.104, D.107, K.152 Ligands: UNL.4, UNL.8, UNL.36 Ligand excluded by PLIP UNL.8: 17 residues within 4Å: Chain A: P.102, P.153, Y.154, H.155, H.156, H.157 Chain B: G.126, G.127, A.128, G.129, H.130, M.148, P.150, L.175, F.179 Ligands: UNL.5, UNL.10 Ligand excluded by PLIP UNL.9: 10 residues within 4Å: Chain B: P.123, V.124, V.125, H.130, V.133, P.134 Chain D: H.130, V.133 Ligands: UNL.22, UNL.35 Ligand excluded by PLIP UNL.10: 7 residues within 4Å: Chain B: S.103, D.107, G.126, S.146, M.148 Ligands: UNL.8, UNL.18 Ligand excluded by PLIP UNL.16: 9 residues within 4Å: Chain A: T.131, Q.135, I.138, H.139 Chain C: T.131, H.139 Chain E: H.139 Ligands: UNL.3, UNL.29 Ligand excluded by PLIP UNL.17: 4 residues within 4Å: Chain C: E.128, P.130, T.131 Ligands: UNL.18 Ligand excluded by PLIP UNL.18: 20 residues within 4Å: Chain A: D.134 Chain B: S.104, D.107, K.152 Chain C: P.102, A.105, S.106, G.109, Q.110, H.113, Y.126, V.127, E.128, H.129, P.130, S.149, H.155 Ligands: UNL.10, UNL.17, UNL.21 Ligand excluded by PLIP UNL.21: 17 residues within 4Å: Chain C: P.102, P.153, Y.154, H.155, H.156, H.157 Chain D: G.126, G.127, A.128, G.129, H.130, M.148, P.150, L.175, F.179 Ligands: UNL.18, UNL.23 Ligand excluded by PLIP UNL.22: 10 residues within 4Å: Chain D: P.123, V.124, V.125, H.130, V.133, P.134 Chain F: H.130, V.133 Ligands: UNL.9, UNL.35 Ligand excluded by PLIP UNL.23: 7 residues within 4Å: Chain D: S.103, D.107, G.126, S.146, M.148 Ligands: UNL.21, UNL.31 Ligand excluded by PLIP UNL.29: 9 residues within 4Å: Chain A: H.139 Chain C: T.131, Q.135, I.138, H.139 Chain E: T.131, H.139 Ligands: UNL.3, UNL.16 Ligand excluded by PLIP UNL.30: 4 residues within 4Å: Chain E: E.128, P.130, T.131 Ligands: UNL.31 Ligand excluded by PLIP UNL.31: 20 residues within 4Å: Chain C: D.134 Chain D: S.104, D.107, K.152 Chain E: P.102, A.105, S.106, G.109, Q.110, H.113, Y.126, V.127, E.128, H.129, P.130, S.149, H.155 Ligands: UNL.23, UNL.30, UNL.34 Ligand excluded by PLIP UNL.34: 17 residues within 4Å: Chain E: P.102, P.153, Y.154, H.155, H.156, H.157 Chain F: G.126, G.127, A.128, G.129, H.130, M.148, P.150, L.175, F.179 Ligands: UNL.31, UNL.36 Ligand excluded by PLIP UNL.35: 10 residues within 4Å: Chain B: H.130, V.133 Chain F: P.123, V.124, V.125, H.130, V.133, P.134 Ligands: UNL.9, UNL.22 Ligand excluded by PLIP UNL.36: 7 residues within 4Å: Chain F: S.103, D.107, G.126, S.146, M.148 Ligands: UNL.5, UNL.34 Ligand excluded by PLIP

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

CL.6: 3 residues within 4Å: Chain A: R.168, R.229 Chain B: T.17 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain C: R.168, R.229 Chain D: T.17 Ligand excluded by PLIP CL.32: 3 residues within 4Å: Chain E: R.168, R.229 Chain F: T.17 Ligand excluded by PLIP

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

PO4.11: 4 residues within 4Å: Chain B: R.209, E.241, H.261, I.265 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.209, B:H.261 PO4.12: 3 residues within 4Å: Chain B: N.68, H.69, A.258 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.69 PO4.13: 2 residues within 4Å: Chain B: R.209, H.261 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.209, B:H.261 PO4.24: 4 residues within 4Å: Chain D: R.209, E.241, H.261, I.265 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:R.209, D:H.261 PO4.25: 3 residues within 4Å: Chain D: N.68, H.69, A.258 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:H.69 PO4.26: 2 residues within 4Å: Chain D: R.209, H.261 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:R.209, D:H.261 PO4.37: 4 residues within 4Å: Chain F: R.209, E.241, H.261, I.265 2 PLIP interactions: 2 interactions with chain F Salt bridges: F:R.209, F:H.261 PO4.38: 3 residues within 4Å: Chain F: N.68, H.69, A.258 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:H.69 PO4.39: 2 residues within 4Å: Chain F: R.209, H.261 2 PLIP interactions: 2 interactions with chain F Salt bridges: F:R.209, F:H.261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aziz, I. et al., The molybdenum storage protein forms and deposits distinct polynuclear tungsten oxygen aggregates. J.Inorg.Biochem. (2022)

Release Date

2022-07-27

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Molybdenum storage protein subunit alpha

Molybdenum storage protein subunit beta

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