SMTL ID : 6gx4.1

The molybdenum storage protein: with ATP/Mn2+ and with POM clusters formed under in vitro conditions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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:Q.45, A:S.46, A:S.46, A:A.77, A:G.78, A:D.189, A:Y.194, A:Y.194, A:N.197, A:K.199, A:K.199 Water bridges: A:N.197, A:N.197 Salt bridges: A:K.41, A:K.41, A:K.188, A:K.188 ATP.5: 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: MN.6 20 PLIP interactions: 20 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:R.48, B:D.170 Salt bridges: B:K.44, B:K.44 ATP.10: 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:Q.45, C:S.46, C:S.46, C:A.77, C:G.78, C:D.189, C:Y.194, C:Y.194, C:N.197, C:K.199, C:K.199 Water bridges: C:N.197, C:N.197 Salt bridges: C:K.41, C:K.41, C:K.188, C:K.188 ATP.14: 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: MN.15 20 PLIP interactions: 20 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:R.48, D:D.170 Salt bridges: D:K.44, D:K.44 ATP.19: 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:Q.45, E:S.46, E:S.46, E:A.77, E:G.78, E:D.189, E:Y.194, E:Y.194, E:N.197, E:K.199, E:K.199 Water bridges: E:N.197, E:N.197 Salt bridges: E:K.41, E:K.41, E:K.188, E:K.188 ATP.23: 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: MN.24 20 PLIP interactions: 20 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:R.48, F:D.170 Salt bridges: F:K.44, F:K.44

6 x FUQ: Mo5 Cluster(Non-covalent)

FUQ.2: 12 residues within 4Å: Chain A: A.128, G.129, L.130, S.131 Chain B: P.102, H.155, H.156 Chain E: D.107, A.111, Q.115, V.124 Ligands: FV2.7 9 PLIP interactions: 3 interactions with chain B, 3 interactions with chain E, 3 interactions with chain A Hydrogen bonds: B:H.155, B:H.156, E:Q.115, E:V.124, A:G.129, A:L.130, A:S.131 Water bridges: B:S.99, E:Q.115 FUQ.3: 8 residues within 4Å: Chain A: D.107, G.126, G.127, A.128, P.150, K.152 Chain B: P.130 Ligands: FV2.16 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.107, A:G.127, A:A.128, A:K.152, A:K.152, A:K.152 Water bridges: A:P.150, A:K.152 FUQ.11: 12 residues within 4Å: Chain A: D.107, A.111, Q.115, V.124 Chain C: A.128, G.129, L.130, S.131 Chain D: P.102, H.155, H.156 Ligands: FV2.16 9 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A, 3 interactions with chain D Hydrogen bonds: C:G.129, C:L.130, C:S.131, A:Q.115, A:V.124, D:H.155, D:H.156 Water bridges: A:Q.115, D:S.99 FUQ.12: 8 residues within 4Å: Chain C: D.107, G.126, G.127, A.128, P.150, K.152 Chain D: P.130 Ligands: FV2.25 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.107, C:G.127, C:A.128, C:K.152, C:K.152, C:K.152 Water bridges: C:P.150, C:K.152 FUQ.20: 12 residues within 4Å: Chain C: D.107, A.111, Q.115, V.124 Chain E: A.128, G.129, L.130, S.131 Chain F: P.102, H.155, H.156 Ligands: FV2.25 9 PLIP interactions: 3 interactions with chain E, 3 interactions with chain F, 3 interactions with chain C Hydrogen bonds: E:G.129, E:L.130, E:S.131, F:H.155, F:H.156, C:Q.115, C:V.124 Water bridges: F:S.99, C:Q.115 FUQ.21: 8 residues within 4Å: Chain E: D.107, G.126, G.127, A.128, P.150, K.152 Chain F: P.130 Ligands: FV2.7 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:D.107, E:G.127, E:A.128, E:K.152, E:K.152, E:K.152 Water bridges: E:P.150, E:K.152

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

PO4.4: 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 PO4.9: 3 residues within 4Å: Chain B: K.31, R.32, A.275 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.32 Water bridges: B:R.32 Salt bridges: B:R.32 PO4.13: 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 PO4.18: 3 residues within 4Å: Chain D: K.31, R.32, A.275 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.32 Water bridges: D:R.32 Salt bridges: D:R.32 PO4.22: 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 PO4.27: 3 residues within 4Å: Chain F: K.31, R.32, A.275 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.32 Water bridges: F:R.32 Salt bridges: F:R.32

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.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.6, H2O.7 MN.15: 4 residues within 4Å: Chain D: D.170, E.189, P.226 Ligands: ATP.14 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.189, D:P.226, H2O.18, H2O.18 MN.24: 4 residues within 4Å: Chain F: D.170, E.189, P.226 Ligands: ATP.23 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.189, F:P.226, H2O.30, H2O.30

3 x FV2: Mo8 cluster(Non-covalent)

FV2.7: 15 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.2, FUQ.21 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:H.129, B:H.129, B:S.149, B:H.155, B:H.155 FV2.16: 15 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.3, FUQ.11 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:H.129, D:H.129, D:S.149, D:H.155, D:H.155 FV2.25: 15 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, FUQ.20 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:H.129, F:H.129, F:S.149, F:H.155, F:H.155

3 x MOO: MOLYBDATE ION(Non-covalent)

MOO.8: 7 residues within 4Å: Chain B: T.131, H.139 Chain D: H.139 Chain F: I.138, H.139 Ligands: MOO.17, MOO.26 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.139 MOO.17: 7 residues within 4Å: Chain B: I.138, H.139 Chain D: T.131, H.139 Chain F: H.139 Ligands: MOO.8, MOO.26 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:H.139 MOO.26: 7 residues within 4Å: Chain B: H.139 Chain D: I.138, H.139 Chain F: T.131, H.139 Ligands: MOO.8, MOO.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Poppe, J. et al., The Molybdenum Storage Protein: A soluble ATP hydrolysis-dependent molybdate pump. FEBS J. (2018)

Release Date

2018-12-05

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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