SMTL ID : 1pvw.3 (2 other biounits)

3,4-dihydroxy-2-butanone 4-phosphate synthase from M. jannaschii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-hexamer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: R.25, E.26, D.30, H.164 Ligands: CA.2, PO4.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.26, A:H.164, H2O.1, H2O.1 ZN.4: 3 residues within 4Å: Chain B: E.128, E.132 Chain F: H.206 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain F Metal complexes: B:E.128, B:E.132, B:E.132, F:H.206 ZN.5: 6 residues within 4Å: Chain D: R.25, E.26, D.30, H.164 Ligands: CA.6, PO4.7 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.26, D:H.164, H2O.1, H2O.1 ZN.8: 3 residues within 4Å: Chain C: H.206 Chain E: E.128, E.132 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain C Metal complexes: E:E.128, E:E.132, E:E.132, C:H.206

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: E.26, Y.95 Ligands: ZN.1, PO4.3 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.26, H2O.1, H2O.1, H2O.1, H2O.1, H2O.1 CA.6: 4 residues within 4Å: Chain D: E.26, Y.95 Ligands: ZN.5, PO4.7 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:E.26, H2O.1, H2O.1, H2O.1, H2O.1, H2O.1

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

PO4.3: 8 residues within 4Å: Chain A: R.25, E.26, R.161, G.163, H.164, T.165 Ligands: ZN.1, CA.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.164, A:T.165, A:T.165 Water bridges: A:E.26 Salt bridges: A:R.25, A:R.161 PO4.7: 8 residues within 4Å: Chain D: R.25, E.26, R.161, G.163, H.164, T.165 Ligands: ZN.5, CA.6 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:H.164, D:T.165 Water bridges: D:E.26 Salt bridges: D:R.25, D:R.161

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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

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

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