SMTL ID : 4z7c.1

Diphosphomevalonate decarboxylase from the Sulfolobus solfataricus, space group h32

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 7 residues within 4Å: Chain A: A.13, K.16, Y.17, S.140, R.143, M.197, D.280 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.17, A:Y.17, A:Y.17, A:S.140 Water bridges: A:A.13, A:R.143 Salt bridges: A:K.16, A:R.143 PO4.3: 10 residues within 4Å: Chain A: E.156, R.157, D.162 Chain B: E.156, R.157, D.162 Chain C: R.157, D.162 Ligands: PO4.7, PO4.11 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:E.156, A:E.156 Salt bridges: B:R.157, A:R.157, C:R.157 PO4.5: 7 residues within 4Å: Chain B: A.13, K.16, Y.17, S.140, R.143, M.197, D.280 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.17, B:Y.17, B:Y.17, B:S.140 Water bridges: B:A.13, B:R.143 Salt bridges: B:K.16, B:R.143 PO4.7: 10 residues within 4Å: Chain A: R.157, D.162 Chain B: E.156, R.157, D.162 Chain C: E.156, R.157, D.162 Ligands: PO4.3, PO4.11 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:E.156, C:E.156 Salt bridges: B:R.157, C:R.157, A:R.157 PO4.9: 7 residues within 4Å: Chain C: A.13, K.16, Y.17, S.140, R.143, M.197, D.280 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Y.17, C:Y.17, C:Y.17, C:S.140 Water bridges: C:A.13, C:R.143 Salt bridges: C:K.16, C:R.143 PO4.11: 10 residues within 4Å: Chain A: E.156, R.157, D.162 Chain B: R.157, D.162 Chain C: E.156, R.157, D.162 Ligands: PO4.3, PO4.7 6 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:E.156, A:D.162, C:E.156 Salt bridges: A:R.157, C:R.157, B:R.157 PO4.13: 7 residues within 4Å: Chain D: A.13, K.16, Y.17, S.140, R.143, M.197, D.280 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:Y.17, D:Y.17, D:Y.17, D:S.140 Water bridges: D:A.13, D:R.143, D:D.280, D:D.280 Salt bridges: D:K.16, D:R.143 PO4.15: 10 residues within 4Å: Chain D: E.156, R.157, D.162 Chain E: E.156, R.157, D.162 Chain F: R.157, D.162 Ligands: PO4.19, PO4.23 9 PLIP interactions: 4 interactions with chain D, 2 interactions with chain F, 3 interactions with chain E Hydrogen bonds: D:E.156, D:D.162, D:D.162, F:D.162, E:D.162, E:D.162 Salt bridges: D:R.157, F:R.157, E:R.157 PO4.17: 7 residues within 4Å: Chain E: A.13, K.16, Y.17, S.140, R.143, M.197, D.280 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:Y.17, E:Y.17, E:Y.17, E:S.140 Water bridges: E:A.13, E:R.143, E:D.280, E:D.280 Salt bridges: E:K.16, E:R.143 PO4.19: 10 residues within 4Å: Chain D: R.157, D.162 Chain E: E.156, R.157, D.162 Chain F: E.156, R.157, D.162 Ligands: PO4.15, PO4.23 7 PLIP interactions: 2 interactions with chain D, 2 interactions with chain F, 3 interactions with chain E Hydrogen bonds: D:D.162, F:D.162, E:D.162, E:D.162 Salt bridges: D:R.157, F:R.157, E:R.157 PO4.21: 7 residues within 4Å: Chain F: A.13, K.16, Y.17, S.140, R.143, M.197, D.280 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:Y.17, F:Y.17, F:Y.17, F:S.140 Water bridges: F:A.13, F:R.143, F:D.280, F:D.280 Salt bridges: F:K.16, F:R.143 PO4.23: 10 residues within 4Å: Chain D: E.156, R.157, D.162 Chain E: R.157, D.162 Chain F: E.156, R.157, D.162 Ligands: PO4.15, PO4.19 7 PLIP interactions: 2 interactions with chain D, 3 interactions with chain F, 2 interactions with chain E Hydrogen bonds: D:D.162, F:E.156, F:D.162, E:D.162 Salt bridges: D:R.157, F:R.157, E:R.157

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

NA.2: 4 residues within 4Å: Chain A: K.47, T.49, K.90, E.92 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.49, A:T.49, A:T.49, A:E.92, A:E.92 NA.6: 4 residues within 4Å: Chain B: K.47, T.49, K.90, E.92 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.49, B:T.49, B:K.90, B:E.92, B:E.92 NA.10: 4 residues within 4Å: Chain C: K.47, T.49, K.90, E.92 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.47, C:T.49, C:T.49, C:E.92, C:E.92 NA.14: 4 residues within 4Å: Chain D: K.47, T.49, K.90, E.92 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.49, D:T.49, D:E.92 NA.18: 4 residues within 4Å: Chain E: K.47, T.49, K.90, E.92 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.49, E:K.90, E:E.92 NA.22: 4 residues within 4Å: Chain F: K.47, T.49, K.90, E.92 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:T.49, F:T.49, F:E.92

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: L.103, A.104, N.284, H.286 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.284 Water bridges: A:D.280, A:H.286 GOL.8: 4 residues within 4Å: Chain B: L.103, A.104, N.284, H.286 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.284 Water bridges: B:D.280, B:H.286 GOL.12: 4 residues within 4Å: Chain C: L.103, A.104, N.284, H.286 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.284 Water bridges: C:D.280, C:H.286 GOL.16: 4 residues within 4Å: Chain D: L.103, A.104, N.284, H.286 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.284 Water bridges: D:D.280, D:H.286 GOL.20: 4 residues within 4Å: Chain E: L.103, A.104, N.284, H.286 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.284 Water bridges: E:D.280, E:H.286 GOL.24: 4 residues within 4Å: Chain F: L.103, A.104, N.284, H.286 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.284 Water bridges: F:D.280, F:H.286

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hattori, A. et al., In Vivo Formation of the Protein Disulfide Bond That Enhances the Thermostability of Diphosphomevalonate Decarboxylase, an Intracellular Enzyme from the Hyperthermophilic Archaeon Sulfolobus solfataricus. J.Bacteriol. (2015)

Release Date

2015-09-16

Peptides

Diphosphomevalonate decarboxylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Diphosphomevalonate decarboxylase

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