SMTL ID : 4ndr.1

Crystal structure Molybdenum Storage Protein with fully Mo-loaded cavity

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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.42, G.44, G.45, Q.46, S.47, G.77, A.78, G.79, T.169, D.170, K.189, D.190, G.193, L.194, Y.195, A.197, N.198, P.199, K.200, S.224, I.225 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.45, A:Q.46, A:Q.46, A:S.47, A:S.47, A:A.78, A:G.79, A:D.190, A:Y.195, A:Y.195, A:K.200, A:K.200 Salt bridges: A:K.42, A:K.42, A:K.189, A:K.189, A:K.189 ATP.20: 24 residues within 4Å: Chain A: S.16 Chain B: K.45, G.47, G.48, R.49, V.50, 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.21 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:G.48, B:R.49, B:V.50, B:A.80, B:G.81, B:R.85, B:N.191, B:N.191, B:Y.196, B:Y.196, B:N.201 Water bridges: B:K.45, B:K.45, B:K.45, B:A.170, B:D.171 Salt bridges: B:K.45, B:K.45 ATP.28: 21 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, G.193, L.194, Y.195, A.197, N.198, P.199, K.200, S.224, I.225 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:G.45, C:Q.46, C:Q.46, C:S.47, C:S.47, C:A.78, C:G.79, C:D.190, C:Y.195, C:Y.195, C:K.200, C:K.200 Salt bridges: C:K.42, C:K.42, C:K.189, C:K.189, C:K.189 ATP.47: 24 residues within 4Å: Chain C: S.16 Chain D: K.45, G.47, G.48, R.49, V.50, 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.48 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:G.48, D:R.49, D:V.50, D:A.80, D:G.81, D:R.85, D:N.191, D:N.191, D:Y.196, D:Y.196, D:N.201 Water bridges: D:K.45, D:K.45, D:K.45, D:A.170, D:D.171 Salt bridges: D:K.45, D:K.45 ATP.55: 21 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, G.193, L.194, Y.195, A.197, N.198, P.199, K.200, S.224, I.225 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:G.45, E:Q.46, E:Q.46, E:S.47, E:S.47, E:A.78, E:G.79, E:D.190, E:Y.195, E:Y.195, E:K.200, E:K.200 Salt bridges: E:K.42, E:K.42, E:K.189, E:K.189, E:K.189 ATP.74: 24 residues within 4Å: Chain E: S.16 Chain F: K.45, G.47, G.48, R.49, V.50, 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.75 18 PLIP interactions: 18 interactions with chain F Hydrogen bonds: F:G.48, F:R.49, F:V.50, F:A.80, F:G.81, F:R.85, F:N.191, F:N.191, F:Y.196, F:Y.196, F:N.201 Water bridges: F:K.45, F:K.45, F:K.45, F:A.170, F:D.171 Salt bridges: F:K.45, F:K.45

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

PO4.2: 4 residues within 4Å: Chain A: R.210, E.242, H.262, I.266 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.242 Salt bridges: A:R.210, A:H.262 PO4.29: 4 residues within 4Å: Chain C: R.210, E.242, H.262, I.266 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.242 Salt bridges: C:R.210, C:H.262 PO4.56: 4 residues within 4Å: Chain E: R.210, E.242, H.262, I.266 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.242 Salt bridges: E:R.210, E:H.262

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

8M0.3: 21 residues within 4Å: Chain A: V.126, G.127, G.128, A.129, G.130, 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: MO.6, MO.8, MO.9, MO.18, 8M0.22 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.128, A:A.129, A:G.130, A:S.147, A:P.150, B:H.156, B:H.157, B:H.157, B:H.158, B:H.158 Water bridges: A:S.147, A:S.147 8M0.22: 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: 8M0.3 9 PLIP interactions: 9 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 Water bridges: B:P.103, B:S.107 8M0.30: 21 residues within 4Å: Chain C: V.126, G.127, G.128, A.129, G.130, 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: MO.33, MO.35, MO.36, MO.45, 8M0.49 12 PLIP interactions: 5 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:H.156, D:H.157, D:H.157, D:H.158, D:H.158, C:G.128, C:A.129, C:G.130, C:S.147, C:P.150 Water bridges: C:S.147, C:S.147 8M0.49: 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: 8M0.30 9 PLIP interactions: 9 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 Water bridges: D:P.103, D:S.107 8M0.57: 21 residues within 4Å: Chain E: V.126, G.127, G.128, A.129, G.130, 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: MO.60, MO.62, MO.63, MO.72, 8M0.76 12 PLIP interactions: 5 interactions with chain F, 7 interactions with chain E Hydrogen bonds: F:H.156, F:H.157, F:H.157, F:H.158, F:H.158, E:G.128, E:A.129, E:G.130, E:S.147, E:P.150 Water bridges: E:S.147, E:S.147 8M0.76: 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: 8M0.57 9 PLIP interactions: 9 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 Water bridges: F:P.103, F:S.107

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

MO.4: 3 residues within 4Å: Ligands: MO.5, MO.8, MO.9 Ligand excluded by PLIP MO.5: 3 residues within 4Å: Ligands: MO.4, MO.6, MO.9 Ligand excluded by PLIP MO.6: 4 residues within 4Å: Ligands: 8M0.3, MO.5, MO.7, MO.9 Ligand excluded by PLIP MO.7: 3 residues within 4Å: Ligands: MO.6, MO.8, MO.9 Ligand excluded by PLIP MO.8: 4 residues within 4Å: Ligands: 8M0.3, MO.4, MO.7, MO.9 Ligand excluded by PLIP MO.9: 6 residues within 4Å: Ligands: 8M0.3, MO.4, MO.5, MO.6, MO.7, MO.8 Ligand excluded by PLIP MO.10: 3 residues within 4Å: Ligands: MO.11, MO.12, MO.38 Ligand excluded by PLIP MO.11: 4 residues within 4Å: Ligands: MO.10, MO.38, MO.64, MO.65 Ligand excluded by PLIP MO.12: 6 residues within 4Å: Chain A: V.126 Ligands: MO.10, MO.13, MO.41, MO.67, MO.68 Ligand excluded by PLIP MO.13: 5 residues within 4Å: Ligands: MO.12, MO.14, MO.39, MO.41, MO.68 Ligand excluded by PLIP MO.14: 7 residues within 4Å: Ligands: MO.13, MO.39, MO.40, MO.41, MO.66, MO.67, MO.68 Ligand excluded by PLIP MO.15: 5 residues within 4Å: Chain D: H.157 Ligands: MO.16, MO.17, MO.45, MO.46 Ligand excluded by PLIP MO.16: 4 residues within 4Å: Chain A: A.112 Ligands: MO.15, MO.17, MO.45 Ligand excluded by PLIP MO.17: 4 residues within 4Å: Ligands: MO.15, MO.16, MO.45, MO.46 Ligand excluded by PLIP MO.18: 5 residues within 4Å: Ligands: 8M0.3, MO.19, MO.69, MO.70, MO.71 Ligand excluded by PLIP MO.19: 3 residues within 4Å: Ligands: MO.18, MO.69, MO.71 Ligand excluded by PLIP MO.24: 6 residues within 4Å: Ligands: MO.25, MO.26, MO.52, MO.53, MO.54, MO.81 Ligand excluded by PLIP MO.25: 9 residues within 4Å: Ligands: MO.24, MO.26, MO.27, MO.52, MO.53, MO.54, MO.78, MO.79, MO.81 Ligand excluded by PLIP MO.26: 6 residues within 4Å: Ligands: MO.24, MO.25, MO.54, MO.78, MO.79, MO.81 Ligand excluded by PLIP MO.27: 9 residues within 4Å: Ligands: MO.25, MO.51, MO.52, MO.53, MO.54, MO.78, MO.79, MO.80, MO.81 Ligand excluded by PLIP MO.31: 3 residues within 4Å: Ligands: MO.32, MO.35, MO.36 Ligand excluded by PLIP MO.32: 3 residues within 4Å: Ligands: MO.31, MO.33, MO.36 Ligand excluded by PLIP MO.33: 4 residues within 4Å: Ligands: 8M0.30, MO.32, MO.34, MO.36 Ligand excluded by PLIP MO.34: 3 residues within 4Å: Ligands: MO.33, MO.35, MO.36 Ligand excluded by PLIP MO.35: 4 residues within 4Å: Ligands: 8M0.30, MO.31, MO.34, MO.36 Ligand excluded by PLIP MO.36: 6 residues within 4Å: Ligands: 8M0.30, MO.31, MO.32, MO.33, MO.34, MO.35 Ligand excluded by PLIP MO.37: 3 residues within 4Å: Ligands: MO.38, MO.39, MO.65 Ligand excluded by PLIP MO.38: 4 residues within 4Å: Ligands: MO.10, MO.11, MO.37, MO.65 Ligand excluded by PLIP MO.39: 6 residues within 4Å: Chain C: V.126 Ligands: MO.13, MO.14, MO.37, MO.40, MO.68 Ligand excluded by PLIP MO.40: 5 residues within 4Å: Ligands: MO.14, MO.39, MO.41, MO.66, MO.68 Ligand excluded by PLIP MO.41: 7 residues within 4Å: Ligands: MO.12, MO.13, MO.14, MO.40, MO.66, MO.67, MO.68 Ligand excluded by PLIP MO.42: 5 residues within 4Å: Chain F: H.157 Ligands: MO.43, MO.44, MO.72, MO.73 Ligand excluded by PLIP MO.43: 4 residues within 4Å: Chain C: A.112 Ligands: MO.42, MO.44, MO.72 Ligand excluded by PLIP MO.44: 4 residues within 4Å: Ligands: MO.42, MO.43, MO.72, MO.73 Ligand excluded by PLIP MO.45: 5 residues within 4Å: Ligands: MO.15, MO.16, MO.17, 8M0.30, MO.46 Ligand excluded by PLIP MO.46: 3 residues within 4Å: Ligands: MO.15, MO.17, MO.45 Ligand excluded by PLIP MO.51: 6 residues within 4Å: Ligands: MO.27, MO.52, MO.53, MO.79, MO.80, MO.81 Ligand excluded by PLIP MO.52: 9 residues within 4Å: Ligands: MO.24, MO.25, MO.27, MO.51, MO.53, MO.54, MO.79, MO.80, MO.81 Ligand excluded by PLIP MO.53: 6 residues within 4Å: Ligands: MO.24, MO.25, MO.27, MO.51, MO.52, MO.81 Ligand excluded by PLIP MO.54: 9 residues within 4Å: Ligands: MO.24, MO.25, MO.26, MO.27, MO.52, MO.78, MO.79, MO.80, MO.81 Ligand excluded by PLIP MO.58: 3 residues within 4Å: Ligands: MO.59, MO.62, MO.63 Ligand excluded by PLIP MO.59: 3 residues within 4Å: Ligands: MO.58, MO.60, MO.63 Ligand excluded by PLIP MO.60: 4 residues within 4Å: Ligands: 8M0.57, MO.59, MO.61, MO.63 Ligand excluded by PLIP MO.61: 3 residues within 4Å: Ligands: MO.60, MO.62, MO.63 Ligand excluded by PLIP MO.62: 4 residues within 4Å: Ligands: 8M0.57, MO.58, MO.61, MO.63 Ligand excluded by PLIP MO.63: 6 residues within 4Å: Ligands: 8M0.57, MO.58, MO.59, MO.60, MO.61, MO.62 Ligand excluded by PLIP MO.64: 3 residues within 4Å: Ligands: MO.11, MO.65, MO.66 Ligand excluded by PLIP MO.65: 4 residues within 4Å: Ligands: MO.11, MO.37, MO.38, MO.64 Ligand excluded by PLIP MO.66: 6 residues within 4Å: Chain E: V.126 Ligands: MO.14, MO.40, MO.41, MO.64, MO.67 Ligand excluded by PLIP MO.67: 5 residues within 4Å: Ligands: MO.12, MO.14, MO.41, MO.66, MO.68 Ligand excluded by PLIP MO.68: 7 residues within 4Å: Ligands: MO.12, MO.13, MO.14, MO.39, MO.40, MO.41, MO.67 Ligand excluded by PLIP MO.69: 5 residues within 4Å: Chain B: H.157 Ligands: MO.18, MO.19, MO.70, MO.71 Ligand excluded by PLIP MO.70: 4 residues within 4Å: Chain E: A.112 Ligands: MO.18, MO.69, MO.71 Ligand excluded by PLIP MO.71: 4 residues within 4Å: Ligands: MO.18, MO.19, MO.69, MO.70 Ligand excluded by PLIP MO.72: 5 residues within 4Å: Ligands: MO.42, MO.43, MO.44, 8M0.57, MO.73 Ligand excluded by PLIP MO.73: 3 residues within 4Å: Ligands: MO.42, MO.44, MO.72 Ligand excluded by PLIP MO.78: 6 residues within 4Å: Ligands: MO.25, MO.26, MO.27, MO.54, MO.79, MO.80 Ligand excluded by PLIP MO.79: 9 residues within 4Å: Ligands: MO.25, MO.26, MO.27, MO.51, MO.52, MO.54, MO.78, MO.80, MO.81 Ligand excluded by PLIP MO.80: 6 residues within 4Å: Ligands: MO.27, MO.51, MO.52, MO.54, MO.78, MO.79 Ligand excluded by PLIP MO.81: 9 residues within 4Å: Ligands: MO.24, MO.25, MO.26, MO.27, MO.51, MO.52, MO.53, MO.54, MO.79 Ligand excluded by PLIP

3 x MG: MAGNESIUM ION(Non-covalent)

MG.21: 4 residues within 4Å: Chain B: D.171, E.190, P.227 Ligands: ATP.20 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.190, B:P.227, H2O.8, H2O.9 MG.48: 4 residues within 4Å: Chain D: D.171, E.190, P.227 Ligands: ATP.47 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.190, D:P.227, H2O.22, H2O.22 MG.75: 4 residues within 4Å: Chain F: D.171, E.190, P.227 Ligands: ATP.74 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.190, F:P.227, H2O.36, H2O.36

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

M10.23: 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: M10.50, M10.77 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:Q.136, F:Q.136, F:H.140 Water bridges: B:Q.136 M10.50: 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: M10.23, M10.77 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Q.136, B:Q.136, B:H.140 Water bridges: D:Q.136 M10.77: 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: M10.23, M10.50 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:Q.136, D:Q.136, D:H.140 Water bridges: F:Q.136

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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