SMTL ID : 5o5w.1

Molybdenum storage protein room-temperature structure determined by serial millisecond crystallography

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-3-3-mer

Ligands

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

ATP.1: 23 residues within 4Å: Chain A: 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 Chain B: S.16 Ligands: MG.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.47, A:G.48, A:R.49, A:A.80, A:G.81, A:R.85, A:N.191, A:N.191, A:Y.196, A:Y.196, A:N.201 Water bridges: A:K.45, A:K.45, A:R.49, A:D.171 Salt bridges: A:K.45, A:K.45, A:R.49 ATP.28: 23 residues within 4Å: Chain C: 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 Chain D: S.16 Ligands: MG.29 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:G.47, C:G.48, C:R.49, C:A.80, C:G.81, C:R.85, C:N.191, C:N.191, C:Y.196, C:Y.196, C:N.201 Water bridges: C:K.45, C:K.45, C:R.49, C:D.171 Salt bridges: C:K.45, C:K.45, C:R.49 ATP.55: 23 residues within 4Å: Chain E: 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 Chain F: S.16 Ligands: MG.56 19 PLIP interactions: 18 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.47, E:G.48, E:R.49, E:A.80, E:G.81, E:R.85, E:N.191, E:N.191, E:Y.196, E:Y.196, E:N.201 Water bridges: E:K.45, E:K.45, E:R.49, E:D.171, F:S.16 Salt bridges: E:K.45, E:K.45, E:R.49

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: K.45, D.171, E.190, P.227 Ligands: ATP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.190, A:P.227, H2O.1, H2O.1 MG.29: 5 residues within 4Å: Chain C: K.45, D.171, E.190, P.227 Ligands: ATP.28 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.190, C:P.227, H2O.8, H2O.8 MG.56: 5 residues within 4Å: Chain E: K.45, D.171, E.190, P.227 Ligands: ATP.55 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.190, E:P.227, H2O.14, H2O.14

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

8M0.3: 15 residues within 4Å: Chain A: P.103, A.106, S.107, G.110, Q.111, H.114, Y.127, E.129, H.130, P.131, S.150, P.153, P.154, H.156 Ligands: 8M0.13 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:A.106, A:Q.111, A:Y.127, A:H.130, A:H.130, A:H.130, A:S.150 Water bridges: A:H.114, A:E.129 8M0.13: 20 residues within 4Å: Chain A: Y.155, H.156, H.157, H.158 Chain B: G.127, G.128, A.129, G.130, F.146, S.147, M.149, P.150, P.151, K.153, L.176, F.180 Ligands: 8M0.3, MO.11, MO.18, MO.24 13 PLIP interactions: 5 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:H.156, A:H.157, A:H.157, A:H.158, A:H.158, B:G.128, B:A.129, B:G.130, B:K.153, B:K.153 Water bridges: B:S.147, B:S.147, B:M.149 8M0.30: 15 residues within 4Å: Chain C: P.103, A.106, S.107, G.110, Q.111, H.114, Y.127, E.129, H.130, P.131, S.150, P.153, P.154, H.156 Ligands: 8M0.40 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:A.106, C:Q.111, C:Y.127, C:H.130, C:H.130, C:H.130, C:S.150 Water bridges: C:H.114, C:E.129 8M0.40: 20 residues within 4Å: Chain C: Y.155, H.156, H.157, H.158 Chain D: G.127, G.128, A.129, G.130, F.146, S.147, M.149, P.150, P.151, K.153, L.176, F.180 Ligands: 8M0.30, MO.38, MO.45, MO.51 13 PLIP interactions: 5 interactions with chain C, 8 interactions with chain D Hydrogen bonds: C:H.156, C:H.157, C:H.157, C:H.158, C:H.158, D:G.128, D:A.129, D:G.130, D:K.153, D:K.153 Water bridges: D:S.147, D:S.147, D:M.149 8M0.57: 15 residues within 4Å: Chain E: P.103, A.106, S.107, G.110, Q.111, H.114, Y.127, E.129, H.130, P.131, S.150, P.153, P.154, H.156 Ligands: 8M0.67 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:A.106, E:Q.111, E:Y.127, E:H.130, E:H.130, E:H.130, E:S.150 Water bridges: E:H.114, E:E.129 8M0.67: 20 residues within 4Å: Chain E: Y.155, H.156, H.157, H.158 Chain F: G.127, G.128, A.129, G.130, F.146, S.147, M.149, P.150, P.151, K.153, L.176, F.180 Ligands: 8M0.57, MO.65, MO.72, MO.78 13 PLIP interactions: 5 interactions with chain E, 8 interactions with chain F Hydrogen bonds: E:H.156, E:H.157, E:H.157, E:H.158, E:H.158, F:G.128, F:A.129, F:G.130, F:K.153, F:K.153 Water bridges: F:S.147, F:S.147, F:M.149

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

M10.4: 7 residues within 4Å: Chain A: T.132, H.140 Chain E: Q.136, I.139, H.140 Ligands: M10.31, M10.58 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Q.136, E:Q.136, E:H.140, E:H.140 Water bridges: E:Q.136 M10.31: 7 residues within 4Å: Chain A: Q.136, I.139, H.140 Chain C: T.132, H.140 Ligands: M10.4, M10.58 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.136, A:Q.136, A:H.140, A:H.140 Water bridges: A:Q.136 M10.58: 7 residues within 4Å: Chain C: Q.136, I.139, H.140 Chain E: T.132, H.140 Ligands: M10.4, M10.31 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.136, C:Q.136, C:H.140, C:H.140 Water bridges: C:Q.136

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

MO.5: 8 residues within 4Å: Ligands: MO.6, MO.7, MO.8, MO.32, MO.35, MO.59, MO.60, MO.62 Ligand excluded by PLIP MO.6: 7 residues within 4Å: Ligands: MO.5, MO.7, MO.8, MO.32, MO.34, MO.35, MO.62 Ligand excluded by PLIP MO.7: 6 residues within 4Å: Ligands: MO.5, MO.6, MO.8, MO.35, MO.60, MO.62 Ligand excluded by PLIP MO.8: 11 residues within 4Å: Ligands: MO.5, MO.6, MO.7, MO.32, MO.33, MO.34, MO.35, MO.59, MO.60, MO.61, MO.62 Ligand excluded by PLIP MO.9: 4 residues within 4Å: Ligands: MO.15, MO.16, MO.18, MO.27 Ligand excluded by PLIP MO.10: 3 residues within 4Å: Chain A: H.157 Ligands: MO.11, MO.12 Ligand excluded by PLIP MO.11: 3 residues within 4Å: Chain A: H.157 Ligands: MO.10, 8M0.13 Ligand excluded by PLIP MO.12: 3 residues within 4Å: Ligands: MO.10, MO.25, MO.26 Ligand excluded by PLIP MO.14: 4 residues within 4Å: Ligands: MO.15, MO.17, MO.18, MO.27 Ligand excluded by PLIP MO.15: 4 residues within 4Å: Ligands: MO.9, MO.14, MO.18, MO.27 Ligand excluded by PLIP MO.16: 4 residues within 4Å: Ligands: MO.9, MO.17, MO.18, MO.27 Ligand excluded by PLIP MO.17: 4 residues within 4Å: Ligands: MO.14, MO.16, MO.18, MO.27 Ligand excluded by PLIP MO.18: 7 residues within 4Å: Ligands: MO.9, 8M0.13, MO.14, MO.15, MO.16, MO.17, MO.27 Ligand excluded by PLIP MO.19: 6 residues within 4Å: Ligands: MO.20, MO.21, MO.23, MO.47, MO.50, MO.77 Ligand excluded by PLIP MO.20: 7 residues within 4Å: Ligands: MO.19, MO.23, MO.47, MO.50, MO.73, MO.74, MO.77 Ligand excluded by PLIP MO.21: 6 residues within 4Å: Ligands: MO.19, MO.22, MO.23, MO.49, MO.50, MO.77 Ligand excluded by PLIP MO.22: 8 residues within 4Å: Chain B: V.134 Ligands: MO.21, MO.23, MO.49, MO.50, MO.75, MO.76, MO.77 Ligand excluded by PLIP MO.23: 14 residues within 4Å: Ligands: MO.19, MO.20, MO.21, MO.22, MO.46, MO.47, MO.48, MO.49, MO.50, MO.73, MO.74, MO.75, MO.76, MO.77 Ligand excluded by PLIP MO.24: 4 residues within 4Å: Chain B: L.131 Ligands: 8M0.13, MO.25, MO.26 Ligand excluded by PLIP MO.25: 3 residues within 4Å: Ligands: MO.12, MO.24, MO.26 Ligand excluded by PLIP MO.26: 3 residues within 4Å: Ligands: MO.12, MO.24, MO.25 Ligand excluded by PLIP MO.27: 6 residues within 4Å: Ligands: MO.9, MO.14, MO.15, MO.16, MO.17, MO.18 Ligand excluded by PLIP MO.32: 8 residues within 4Å: Ligands: MO.5, MO.6, MO.8, MO.33, MO.34, MO.35, MO.59, MO.62 Ligand excluded by PLIP MO.33: 7 residues within 4Å: Ligands: MO.8, MO.32, MO.34, MO.35, MO.59, MO.61, MO.62 Ligand excluded by PLIP MO.34: 6 residues within 4Å: Ligands: MO.6, MO.8, MO.32, MO.33, MO.35, MO.62 Ligand excluded by PLIP MO.35: 11 residues within 4Å: Ligands: MO.5, MO.6, MO.7, MO.8, MO.32, MO.33, MO.34, MO.59, MO.60, MO.61, MO.62 Ligand excluded by PLIP MO.36: 4 residues within 4Å: Ligands: MO.42, MO.43, MO.45, MO.54 Ligand excluded by PLIP MO.37: 3 residues within 4Å: Chain C: H.157 Ligands: MO.38, MO.39 Ligand excluded by PLIP MO.38: 3 residues within 4Å: Chain C: H.157 Ligands: MO.37, 8M0.40 Ligand excluded by PLIP MO.39: 3 residues within 4Å: Ligands: MO.37, MO.52, MO.53 Ligand excluded by PLIP MO.41: 4 residues within 4Å: Ligands: MO.42, MO.44, MO.45, MO.54 Ligand excluded by PLIP MO.42: 4 residues within 4Å: Ligands: MO.36, MO.41, MO.45, MO.54 Ligand excluded by PLIP MO.43: 4 residues within 4Å: Ligands: MO.36, MO.44, MO.45, MO.54 Ligand excluded by PLIP MO.44: 4 residues within 4Å: Ligands: MO.41, MO.43, MO.45, MO.54 Ligand excluded by PLIP MO.45: 7 residues within 4Å: Ligands: MO.36, 8M0.40, MO.41, MO.42, MO.43, MO.44, MO.54 Ligand excluded by PLIP MO.46: 6 residues within 4Å: Ligands: MO.23, MO.47, MO.48, MO.50, MO.74, MO.77 Ligand excluded by PLIP MO.47: 7 residues within 4Å: Ligands: MO.19, MO.20, MO.23, MO.46, MO.50, MO.74, MO.77 Ligand excluded by PLIP MO.48: 6 residues within 4Å: Ligands: MO.23, MO.46, MO.49, MO.50, MO.76, MO.77 Ligand excluded by PLIP MO.49: 8 residues within 4Å: Chain D: V.134 Ligands: MO.21, MO.22, MO.23, MO.48, MO.50, MO.76, MO.77 Ligand excluded by PLIP MO.50: 14 residues within 4Å: Ligands: MO.19, MO.20, MO.21, MO.22, MO.23, MO.46, MO.47, MO.48, MO.49, MO.73, MO.74, MO.75, MO.76, MO.77 Ligand excluded by PLIP MO.51: 4 residues within 4Å: Chain D: L.131 Ligands: 8M0.40, MO.52, MO.53 Ligand excluded by PLIP MO.52: 3 residues within 4Å: Ligands: MO.39, MO.51, MO.53 Ligand excluded by PLIP MO.53: 3 residues within 4Å: Ligands: MO.39, MO.51, MO.52 Ligand excluded by PLIP MO.54: 6 residues within 4Å: Ligands: MO.36, MO.41, MO.42, MO.43, MO.44, MO.45 Ligand excluded by PLIP MO.59: 8 residues within 4Å: Ligands: MO.5, MO.8, MO.32, MO.33, MO.35, MO.60, MO.61, MO.62 Ligand excluded by PLIP MO.60: 7 residues within 4Å: Ligands: MO.5, MO.7, MO.8, MO.35, MO.59, MO.61, MO.62 Ligand excluded by PLIP MO.61: 6 residues within 4Å: Ligands: MO.8, MO.33, MO.35, MO.59, MO.60, MO.62 Ligand excluded by PLIP MO.62: 11 residues within 4Å: Ligands: MO.5, MO.6, MO.7, MO.8, MO.32, MO.33, MO.34, MO.35, MO.59, MO.60, MO.61 Ligand excluded by PLIP MO.63: 4 residues within 4Å: Ligands: MO.69, MO.70, MO.72, MO.81 Ligand excluded by PLIP MO.64: 3 residues within 4Å: Chain E: H.157 Ligands: MO.65, MO.66 Ligand excluded by PLIP MO.65: 3 residues within 4Å: Chain E: H.157 Ligands: MO.64, 8M0.67 Ligand excluded by PLIP MO.66: 3 residues within 4Å: Ligands: MO.64, MO.79, MO.80 Ligand excluded by PLIP MO.68: 4 residues within 4Å: Ligands: MO.69, MO.71, MO.72, MO.81 Ligand excluded by PLIP MO.69: 4 residues within 4Å: Ligands: MO.63, MO.68, MO.72, MO.81 Ligand excluded by PLIP MO.70: 4 residues within 4Å: Ligands: MO.63, MO.71, MO.72, MO.81 Ligand excluded by PLIP MO.71: 4 residues within 4Å: Ligands: MO.68, MO.70, MO.72, MO.81 Ligand excluded by PLIP MO.72: 7 residues within 4Å: Ligands: MO.63, 8M0.67, MO.68, MO.69, MO.70, MO.71, MO.81 Ligand excluded by PLIP MO.73: 6 residues within 4Å: Ligands: MO.20, MO.23, MO.50, MO.74, MO.75, MO.77 Ligand excluded by PLIP MO.74: 7 residues within 4Å: Ligands: MO.20, MO.23, MO.46, MO.47, MO.50, MO.73, MO.77 Ligand excluded by PLIP MO.75: 6 residues within 4Å: Ligands: MO.22, MO.23, MO.50, MO.73, MO.76, MO.77 Ligand excluded by PLIP MO.76: 8 residues within 4Å: Chain F: V.134 Ligands: MO.22, MO.23, MO.48, MO.49, MO.50, MO.75, MO.77 Ligand excluded by PLIP MO.77: 14 residues within 4Å: Ligands: MO.19, MO.20, MO.21, MO.22, MO.23, MO.46, MO.47, MO.48, MO.49, MO.50, MO.73, MO.74, MO.75, MO.76 Ligand excluded by PLIP MO.78: 4 residues within 4Å: Chain F: L.131 Ligands: 8M0.67, MO.79, MO.80 Ligand excluded by PLIP MO.79: 3 residues within 4Å: Ligands: MO.66, MO.78, MO.80 Ligand excluded by PLIP MO.80: 3 residues within 4Å: Ligands: MO.66, MO.78, MO.79 Ligand excluded by PLIP MO.81: 6 residues within 4Å: Ligands: MO.63, MO.68, MO.69, MO.70, MO.71, MO.72 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weinert, T. et al., Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons. Nat Commun (2017)

Release Date

2017-09-27

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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