SMTL ID : 6rj4.1

Molybdenum storage protein - P6422, ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-6-6-mer

Ligands

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 15 residues within 4Å: Chain A: K.41, G.43, G.44, Q.45, S.46, K.188, G.192, L.193, Y.194, A.196, N.197, P.198, K.199, S.223 Ligands: PO4.2 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:G.44, A:Q.45, A:S.46, A:S.46, A:Y.194, A:Y.194, A:N.197, A:K.199, A:S.223 Water bridges: A:K.41, A:K.41, A:K.41, A:K.41, A:K.188, A:K.188, A:K.188, A:N.197, A:N.197, A:K.199, A:K.199, A:K.199, A:K.199 Salt bridges: A:K.41, A:K.188, A:K.188 ADP.8: 19 residues within 4Å: Chain C: K.41, G.43, G.44, Q.45, S.46, K.188, D.189, E.190, G.192, L.193, Y.194, A.196, N.197, P.198, K.199, L.220, S.223, I.224 Ligands: MG.9 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:G.44, C:Q.45, C:S.46, C:S.46, C:D.189, C:Y.194, C:Y.194, C:N.197, C:K.199, C:K.199 Water bridges: C:K.41, C:K.41, C:K.41, C:K.188, C:K.188, C:N.197, C:N.197 Salt bridges: C:K.41, C:K.188, C:K.188 ADP.13: 12 residues within 4Å: Chain E: Q.45, R.82, K.188, G.192, L.193, Y.194, A.196, N.197, P.198, S.223, I.224 Ligands: PO4.15 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:Q.45, E:Q.45, E:R.82, E:K.188, E:Y.194, E:Y.194, E:N.197, E:I.224 Water bridges: E:K.199, E:K.199 Salt bridges: E:R.82 ADP.18: 15 residues within 4Å: Chain G: K.41, G.43, G.44, Q.45, S.46, K.188, G.192, L.193, Y.194, A.196, N.197, P.198, K.199, S.223 Ligands: PO4.19 25 PLIP interactions: 25 interactions with chain G Hydrogen bonds: G:G.44, G:Q.45, G:S.46, G:S.46, G:Y.194, G:Y.194, G:N.197, G:K.199, G:S.223 Water bridges: G:K.41, G:K.41, G:T.168, G:T.168, G:K.188, G:K.188, G:K.188, G:N.197, G:N.197, G:K.199, G:K.199, G:K.199, G:K.199 Salt bridges: G:K.41, G:K.188, G:K.188 ADP.25: 19 residues within 4Å: Chain I: K.41, G.43, G.44, Q.45, S.46, K.188, D.189, E.190, G.192, L.193, Y.194, A.196, N.197, P.198, K.199, L.220, S.223, I.224 Ligands: MG.26 20 PLIP interactions: 20 interactions with chain I Hydrogen bonds: I:G.44, I:Q.45, I:S.46, I:S.46, I:D.189, I:Y.194, I:Y.194, I:N.197, I:K.199, I:K.199 Water bridges: I:K.41, I:K.41, I:T.168, I:K.188, I:K.188, I:N.197, I:N.197 Salt bridges: I:K.41, I:K.188, I:K.188 ADP.30: 12 residues within 4Å: Chain K: Q.45, R.82, K.188, G.192, L.193, Y.194, A.196, N.197, P.198, S.223, I.224 Ligands: PO4.32 11 PLIP interactions: 11 interactions with chain K Hydrogen bonds: K:Q.45, K:Q.45, K:R.82, K:K.188, K:Y.194, K:Y.194, K:N.197, K:I.224 Water bridges: K:K.199, K:K.199 Salt bridges: K:R.82

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

PO4.2: 7 residues within 4Å: Chain A: K.41, G.43, G.44, Q.45, S.46, K.188 Ligands: ADP.1 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.44, A:Q.45, A:S.46, A:S.46, A:S.46 Water bridges: A:K.41, A:K.41, A:K.41, A:T.168, A:K.188, A:K.188, A:K.188 Salt bridges: A:K.41, A:K.188 PO4.3: 5 residues within 4Å: Chain A: A.77, G.78, A.81, R.167, T.168 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:A.77, A:G.78, A:T.168, A:T.168, A:T.168 Water bridges: A:K.41, A:K.41, A:T.168 Salt bridges: A:K.41, A:R.167 PO4.4: 2 residues within 4Å: Chain A: R.240, S.269 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.269, A:S.269, A:S.269 Salt bridges: A:R.240 PO4.10: 6 residues within 4Å: Chain C: A.77, G.78, A.81, R.167, T.168 Ligands: MG.9 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:A.77, C:G.78, C:T.168, C:T.168, C:E.226, C:E.226 Water bridges: C:Q.45, C:R.167, C:T.168, C:T.168 Salt bridges: C:K.41, C:R.167 PO4.14: 5 residues within 4Å: Chain E: A.77, G.78, R.167, T.168, E.226 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:A.77, E:G.78, E:T.168, E:T.168, E:T.168 Water bridges: E:K.41, E:K.41, E:K.41, E:K.41 Salt bridges: E:K.41, E:R.167 PO4.15: 7 residues within 4Å: Chain E: K.41, G.43, G.44, Q.45, S.46, K.188 Ligands: ADP.13 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:G.44, E:Q.45, E:S.46 Water bridges: E:K.41, E:K.41, E:D.169, E:D.169, E:I.224 Salt bridges: E:K.41, E:K.188 PO4.19: 7 residues within 4Å: Chain G: K.41, G.43, G.44, Q.45, S.46, K.188 Ligands: ADP.18 13 PLIP interactions: 13 interactions with chain G Hydrogen bonds: G:G.44, G:Q.45, G:S.46, G:S.46, G:S.46 Water bridges: G:K.41, G:K.41, G:K.41, G:K.188, G:K.188, G:K.188 Salt bridges: G:K.41, G:K.188 PO4.20: 5 residues within 4Å: Chain G: A.77, G.78, A.81, R.167, T.168 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:A.77, G:G.78, G:T.168, G:T.168, G:T.168, G:T.168 Water bridges: G:K.41, G:K.41, G:E.226 Salt bridges: G:K.41, G:R.167 PO4.21: 2 residues within 4Å: Chain G: R.240, S.269 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:S.269, G:S.269, G:S.269 Salt bridges: G:R.240 PO4.27: 6 residues within 4Å: Chain I: A.77, G.78, A.81, R.167, T.168 Ligands: MG.26 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:A.77, I:G.78, I:T.168, I:T.168, I:T.168, I:E.226 Water bridges: I:K.41, I:K.41, I:Q.45, I:R.167 Salt bridges: I:K.41, I:R.167 PO4.31: 5 residues within 4Å: Chain K: A.77, G.78, R.167, T.168, E.226 10 PLIP interactions: 10 interactions with chain K Hydrogen bonds: K:A.77, K:G.78, K:T.168, K:T.168 Water bridges: K:K.41, K:K.41, K:K.41, K:K.41 Salt bridges: K:K.41, K:R.167 PO4.32: 7 residues within 4Å: Chain K: K.41, G.43, G.44, Q.45, S.46, K.188 Ligands: ADP.30 11 PLIP interactions: 11 interactions with chain K Hydrogen bonds: K:G.44, K:Q.45, K:S.46 Water bridges: K:K.41, K:K.41, K:T.168, K:D.169, K:D.169, K:I.224 Salt bridges: K:K.41, K:K.188

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 6 residues within 4Å: Chain A: G.114, A.118, I.122, P.123, V.124 Chain C: P.134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.122, A:V.124 NA.22: 6 residues within 4Å: Chain G: G.114, A.118, I.122, P.123, V.124 Chain I: P.134 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:I.122, G:V.124

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

ATP.6: 24 residues within 4Å: Chain A: S.15 Chain B: K.44, G.46, G.47, R.48, 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: MG.7 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:N.200, B:N.200, B:P.224 Water bridges: B:K.44, B:K.44, B:K.44, B:D.170, B:D.170 Salt bridges: B:K.44, B:K.44 ATP.11: 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: MG.12 19 PLIP interactions: 18 interactions with chain D, 1 interactions with chain C 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 Water bridges: D:K.44, D:K.44, D:K.44, D:D.170, C:S.15 Salt bridges: D:K.44, D:K.44 ATP.16: 24 residues within 4Å: Chain E: S.15 Chain F: K.44, G.46, G.47, R.48, 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: MG.17 22 PLIP interactions: 21 interactions with chain F, 1 interactions with chain E 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 Water bridges: F:K.44, F:K.44, F:R.84, F:D.170, F:D.170, F:E.189, F:P.226, E:L.16 Salt bridges: F:K.44, F:K.44 ATP.23: 24 residues within 4Å: Chain G: S.15 Chain H: K.44, G.46, G.47, R.48, 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: MG.24 20 PLIP interactions: 20 interactions with chain H Hydrogen bonds: H:G.46, H:G.47, H:R.48, H:V.49, H:A.79, H:G.80, H:R.84, H:N.190, H:N.190, H:Y.195, H:N.200, H:N.200, H:P.224 Water bridges: H:K.44, H:K.44, H:K.44, H:D.170, H:D.170 Salt bridges: H:K.44, H:K.44 ATP.28: 25 residues within 4Å: Chain I: S.15 Chain J: 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: MG.29 20 PLIP interactions: 1 interactions with chain I, 19 interactions with chain J Water bridges: I:S.15, J:K.44, J:K.44, J:K.44, J:D.170 Hydrogen bonds: J:G.46, J:G.47, J:R.48, J:V.49, 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 Salt bridges: J:K.44, J:K.44 ATP.33: 24 residues within 4Å: Chain K: S.15 Chain L: K.44, G.46, G.47, R.48, 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: MG.34 23 PLIP interactions: 22 interactions with chain L, 1 interactions with chain K Hydrogen bonds: L:G.46, L:G.47, L:R.48, L:V.49, 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:K.44, L:R.84, L:D.170, L:D.170, L:E.189, L:P.226, K:L.16 Salt bridges: L:K.44, L:K.44

8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.7: 5 residues within 4Å: Chain B: K.44, D.170, E.189, P.226 Ligands: ATP.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.189, B:P.226, H2O.6, H2O.7 MG.9: 2 residues within 4Å: Ligands: ADP.8, PO4.10 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain D: K.44, D.170, E.189, P.226 Ligands: ATP.11 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.189, D:P.226, H2O.17, H2O.17 MG.17: 5 residues within 4Å: Chain F: K.44, D.170, E.189, P.226 Ligands: ATP.16 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.189, F:P.226, H2O.26, H2O.27 MG.24: 5 residues within 4Å: Chain H: K.44, D.170, E.189, P.226 Ligands: ATP.23 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.189, H:P.226, H2O.37, H2O.37 MG.26: 2 residues within 4Å: Ligands: ADP.25, PO4.27 No protein-ligand interaction detected (PLIP) MG.29: 5 residues within 4Å: Chain J: K.44, D.170, E.189, P.226 Ligands: ATP.28 4 PLIP interactions: 2 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.189, J:P.226, H2O.47, H2O.48 MG.34: 5 residues within 4Å: Chain L: K.44, D.170, E.189, P.226 Ligands: ATP.33 4 PLIP interactions: 2 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.189, L:P.226, H2O.57, H2O.57

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
D

E
F

G
B

I
D

K
F

B
A

D
C

F
E

H
A

J
C

L
E

Molybdenum storage protein subunit beta

Molybdenum storage protein subunit alpha

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