SMTL ID : 6ris.1

The Kb42S variant of the molybdenum storage protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-6-6-mer

Ligands

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

ATP.1: 19 residues within 4Å: Chain A: 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, S.223, I.224 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.44, A:Q.45, A:Q.45, A:S.46, A:A.77, A:T.168, 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:R.167, A:T.168, A:T.168, A:N.197, A:N.197 Salt bridges: A:K.188 ATP.4: 22 residues within 4Å: Chain B: K.44, G.46, G.47, R.48, 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.5 17 PLIP interactions: 2 interactions with chain A, 15 interactions with chain B Water bridges: A:S.15, A:L.16, B:K.44, B:R.84, B:D.170 Hydrogen bonds: B:G.47, B:R.48, B:A.79, B:G.80, B:R.84, B:N.190, B:N.190, B:Y.195, B:Y.195, B:N.200 Salt bridges: B:K.44, B:K.44 ATP.10: 19 residues within 4Å: Chain C: 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, S.223, I.224 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:G.44, C:Q.45, C:Q.45, C:S.46, C:A.77, C:T.168, 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:R.167, C:T.168, C:T.168, C:N.197, C:N.197 Salt bridges: C:K.188 ATP.13: 22 residues within 4Å: Chain D: K.44, G.46, G.47, R.48, 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.14 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.47, D:R.48, D:A.79, D:G.80, D:R.84, D:N.190, D:N.190, D:Y.195, D:Y.195, D:N.200 Water bridges: D:K.44, D:R.84, D:D.170, C:S.15, C:L.16 Salt bridges: D:K.44, D:K.44 ATP.19: 19 residues within 4Å: Chain E: 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, S.223, I.224 21 PLIP interactions: 21 interactions with chain E Hydrogen bonds: E:G.44, E:Q.45, E:Q.45, E:S.46, E:A.77, E:T.168, 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:R.167, E:T.168, E:T.168, E:N.197, E:N.197 Salt bridges: E:K.188 ATP.22: 22 residues within 4Å: Chain F: K.44, G.46, G.47, R.48, 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.23 17 PLIP interactions: 15 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:G.47, F:R.48, F:A.79, F:G.80, F:R.84, F:N.190, F:N.190, F:Y.195, F:Y.195, F:N.200 Water bridges: F:K.44, F:R.84, F:D.170, E:S.15, E:L.16 Salt bridges: F:K.44, F:K.44 ATP.28: 19 residues within 4Å: Chain G: 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, S.223, I.224 21 PLIP interactions: 21 interactions with chain G Hydrogen bonds: G:G.44, G:Q.45, G:Q.45, G:S.46, G:A.77, G:T.168, G:T.168, G:T.168, G:D.189, G:Y.194, G:Y.194, G:N.197, G:K.199, G:K.199 Water bridges: G:G.78, G:G.78, G:R.167, G:T.168, G:N.197, G:N.197 Salt bridges: G:K.188 ATP.31: 22 residues within 4Å: Chain H: K.44, G.46, G.47, R.48, 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.32 18 PLIP interactions: 16 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:G.47, H:R.48, H:A.79, H:G.80, H:R.84, H:E.189, H:N.190, H:N.190, H:Y.195, H:Y.195, H:N.200 Water bridges: H:K.44, H:R.84, H:D.170, G:S.15, G:L.16 Salt bridges: H:K.44, H:K.44 ATP.37: 19 residues within 4Å: Chain I: 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, S.223, I.224 21 PLIP interactions: 21 interactions with chain I Hydrogen bonds: I:G.44, I:Q.45, I:Q.45, I:S.46, I:A.77, I:T.168, I:T.168, I:T.168, I:D.189, I:Y.194, I:Y.194, I:N.197, I:K.199, I:K.199 Water bridges: I:G.78, I:G.78, I:R.167, I:T.168, I:N.197, I:N.197 Salt bridges: I:K.188 ATP.40: 22 residues within 4Å: Chain J: K.44, G.46, G.47, R.48, 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.41 18 PLIP interactions: 16 interactions with chain J, 2 interactions with chain I Hydrogen bonds: J:G.47, J:R.48, J:A.79, J:G.80, J:R.84, J:E.189, J:N.190, J:N.190, J:Y.195, J:Y.195, J:N.200 Water bridges: J:K.44, J:R.84, J:D.170, I:S.15, I:L.16 Salt bridges: J:K.44, J:K.44 ATP.46: 19 residues within 4Å: Chain K: 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, S.223, I.224 21 PLIP interactions: 21 interactions with chain K Hydrogen bonds: K:G.44, K:Q.45, K:Q.45, K:S.46, K:A.77, K:T.168, K:T.168, K:T.168, K:D.189, K:Y.194, K:Y.194, K:N.197, K:K.199, K:K.199 Water bridges: K:G.78, K:G.78, K:R.167, K:T.168, K:N.197, K:N.197 Salt bridges: K:K.188 ATP.49: 22 residues within 4Å: Chain L: K.44, G.46, G.47, R.48, 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.50 18 PLIP interactions: 16 interactions with chain L, 2 interactions with chain K Hydrogen bonds: L:G.47, L:R.48, L:A.79, L:G.80, L:R.84, L:E.189, L:N.190, L:N.190, L:Y.195, L:Y.195, L:N.200 Water bridges: L:K.44, L:R.84, L:D.170, K:S.15, K:L.16 Salt bridges: L:K.44, L:K.44

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

PO4.2: 4 residues within 4Å: Chain A: R.209, E.241, H.261, I.265 Ligand excluded by PLIP PO4.3: 2 residues within 4Å: Chain A: R.209, H.261 Ligand excluded by PLIP PO4.7: 7 residues within 4Å: Chain A: A.128, L.130, P.150 Chain B: Y.154, H.155, H.156, H.157 Ligand excluded by PLIP PO4.8: 5 residues within 4Å: Chain A: A.128 Chain B: H.129, P.153, H.155 Ligands: PO4.9 Ligand excluded by PLIP PO4.9: 5 residues within 4Å: Chain B: Y.126, E.128, H.129, S.149 Ligands: PO4.8 Ligand excluded by PLIP PO4.11: 4 residues within 4Å: Chain C: R.209, E.241, H.261, I.265 Ligand excluded by PLIP PO4.12: 2 residues within 4Å: Chain C: R.209, H.261 Ligand excluded by PLIP PO4.16: 7 residues within 4Å: Chain C: A.128, L.130, P.150 Chain D: Y.154, H.155, H.156, H.157 Ligand excluded by PLIP PO4.17: 5 residues within 4Å: Chain C: A.128 Chain D: H.129, P.153, H.155 Ligands: PO4.18 Ligand excluded by PLIP PO4.18: 5 residues within 4Å: Chain D: Y.126, E.128, H.129, S.149 Ligands: PO4.17 Ligand excluded by PLIP PO4.20: 4 residues within 4Å: Chain E: R.209, E.241, H.261, I.265 Ligand excluded by PLIP PO4.21: 2 residues within 4Å: Chain E: R.209, H.261 Ligand excluded by PLIP PO4.25: 7 residues within 4Å: Chain E: A.128, L.130, P.150 Chain F: Y.154, H.155, H.156, H.157 Ligand excluded by PLIP PO4.26: 5 residues within 4Å: Chain E: A.128 Chain F: H.129, P.153, H.155 Ligands: PO4.27 Ligand excluded by PLIP PO4.27: 5 residues within 4Å: Chain F: Y.126, E.128, H.129, S.149 Ligands: PO4.26 Ligand excluded by PLIP PO4.29: 4 residues within 4Å: Chain G: R.209, E.241, H.261, I.265 Ligand excluded by PLIP PO4.30: 2 residues within 4Å: Chain G: R.209, H.261 Ligand excluded by PLIP PO4.34: 7 residues within 4Å: Chain G: A.128, L.130, P.150 Chain H: Y.154, H.155, H.156, H.157 Ligand excluded by PLIP PO4.35: 5 residues within 4Å: Chain G: A.128 Chain H: H.129, P.153, H.155 Ligands: PO4.36 Ligand excluded by PLIP PO4.36: 5 residues within 4Å: Chain H: Y.126, E.128, H.129, S.149 Ligands: PO4.35 Ligand excluded by PLIP PO4.38: 4 residues within 4Å: Chain I: R.209, E.241, H.261, I.265 Ligand excluded by PLIP PO4.39: 2 residues within 4Å: Chain I: R.209, H.261 Ligand excluded by PLIP PO4.43: 7 residues within 4Å: Chain I: A.128, L.130, P.150 Chain J: Y.154, H.155, H.156, H.157 Ligand excluded by PLIP PO4.44: 5 residues within 4Å: Chain I: A.128 Chain J: H.129, P.153, H.155 Ligands: PO4.45 Ligand excluded by PLIP PO4.45: 5 residues within 4Å: Chain J: Y.126, E.128, H.129, S.149 Ligands: PO4.44 Ligand excluded by PLIP PO4.47: 4 residues within 4Å: Chain K: R.209, E.241, H.261, I.265 Ligand excluded by PLIP PO4.48: 2 residues within 4Å: Chain K: R.209, H.261 Ligand excluded by PLIP PO4.52: 7 residues within 4Å: Chain K: A.128, L.130, P.150 Chain L: Y.154, H.155, H.156, H.157 Ligand excluded by PLIP PO4.53: 5 residues within 4Å: Chain K: A.128 Chain L: H.129, P.153, H.155 Ligands: PO4.54 Ligand excluded by PLIP PO4.54: 5 residues within 4Å: Chain L: Y.126, E.128, H.129, S.149 Ligands: PO4.53 Ligand excluded by PLIP

6 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain B: D.170, E.189, P.226 Ligands: ATP.4 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.189, B:P.226, H2O.6, H2O.6 MG.14: 4 residues within 4Å: Chain D: D.170, E.189, P.226 Ligands: ATP.13 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.189, D:P.226, H2O.15, H2O.16 MG.23: 4 residues within 4Å: Chain F: D.170, E.189, P.226 Ligands: ATP.22 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.189, F:P.226, H2O.25, H2O.26 MG.32: 4 residues within 4Å: Chain H: D.170, E.189, P.226 Ligands: ATP.31 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.189, H:P.226, H2O.35, H2O.35 MG.41: 4 residues within 4Å: Chain J: D.170, E.189, P.226 Ligands: ATP.40 4 PLIP interactions: 2 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.189, J:P.226, H2O.45, H2O.45 MG.50: 4 residues within 4Å: Chain L: D.170, E.189, P.226 Ligands: ATP.49 4 PLIP interactions: 2 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.189, L:P.226, H2O.55, H2O.55

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

CL.6: 3 residues within 4Å: Chain A: T.17 Chain B: R.168, R.229 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain C: T.17 Chain D: R.168, R.229 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain E: T.17 Chain F: R.168, R.229 Ligand excluded by PLIP CL.33: 3 residues within 4Å: Chain G: T.17 Chain H: R.168, R.229 Ligand excluded by PLIP CL.42: 3 residues within 4Å: Chain I: T.17 Chain J: R.168, R.229 Ligand excluded by PLIP CL.51: 3 residues within 4Å: Chain K: T.17 Chain L: R.168, R.229 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brunle, S. et al., Molybdate pumping into the molybdenum storage protein via an ATP-powered piercing mechanism. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-12-18

Peptides

Molybdenum storage protein subunit beta: ACEGIK
Molybdenum storage protein subunit alpha: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
B

E
B

G
B

I
B

K
B

B
A

D
A

F
A

H
A

J
A

L
A

Molybdenum storage protein subunit beta

Molybdenum storage protein subunit alpha

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