SMTL ID : 1pvy.1

3,4-dihydroxy-2-butanone 4-phosphate synthase from M. jannaschii in complex with ribulose 5-phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x 5RP: RIBULOSE-5-PHOSPHATE(Non-covalent)

5RP.1: 15 residues within 4Å: Chain A: R.25, E.26, D.30, C.55, Y.95, S.100, L.151, R.161, G.163, H.164, T.165, I.183, E.185 Ligands: ZN.2, CA.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.95, A:S.100, A:H.164, A:T.165, A:E.185 Salt bridges: A:R.25, A:R.161 5RP.7: 15 residues within 4Å: Chain B: R.25, E.26, D.30, C.55, S.100, F.101, L.151, R.161, G.163, H.164, T.165, I.183, E.185 Ligands: ZN.8, CA.9 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.30, B:S.100, B:H.164, B:T.165 Water bridges: B:E.26, B:E.28, B:R.161 Salt bridges: B:R.25, B:R.161

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: E.26, D.30, H.164 Ligands: 5RP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.26, A:H.164, H2O.6 ZN.6: 1 residues within 4Å: Chain A: H.206 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.206 ZN.8: 3 residues within 4Å: Chain B: E.26, H.164 Ligands: 5RP.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.26, B:H.164, H2O.14

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: E.26, Y.95 Ligands: 5RP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.26, A:Y.95, H2O.6 CA.4: 2 residues within 4Å: Chain A: D.96, E.97 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.97, H2O.2, H2O.3, H2O.3, H2O.4 CA.5: 2 residues within 4Å: Chain A: E.204, N.207 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.204, H2O.4 CA.9: 2 residues within 4Å: Chain B: E.26 Ligands: 5RP.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.26, H2O.12, H2O.14, H2O.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Steinbacher, S. et al., Structure of 3,4-Dihydroxy-2-butanone 4-Phosphate Synthase from Methanococcus jannaschii inComplex with Divalent Metal Ions and the Substrate Ribulose 5-Phosphate: IMPLICATIONS FOR THE CATALYTIC MECHANISM. J.Biol.Chem. (2003)

Release Date

2003-11-04

Peptides

3,4-dihydroxy-2-butanone 4-phosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3,4-dihydroxy-2-butanone 4-phosphate synthase

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