SMTL ID : 1snn.1

3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

5RP.1: 16 residues within 4Å: Chain A: R.25, E.26, D.30, C.55, Y.95, S.100, F.101, L.151, R.161, G.163, H.164, T.165, I.183, E.185 Ligands: ZN.2, CA.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.95, A:S.100, A:H.164, A:T.165 Water bridges: A:E.26, A:E.26, A:S.100, A:R.161, A:E.185 Salt bridges: A:R.25, A:R.161 5RP.7: 16 residues within 4Å: Chain B: R.25, E.26, D.30, L.53, 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 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.100, B:H.164, B:T.165, B:E.185 Water bridges: B:E.28, B:S.100, B:R.161, B:R.161 Salt bridges: B:R.25, B:R.161

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: E.26, D.30, H.164 Ligands: 5RP.1, CA.3 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: 4 residues within 4Å: Chain A: E.26, Y.95 Ligands: 5RP.1, ZN.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.26, A:Y.95, H2O.3, H2O.6 CA.4: 2 residues within 4Å: Chain A: D.96, E.97 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.96, A:E.97, 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., Metal sites in 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with the substrate ribulose 5-phosphate. Acta Crystallogr.,Sect.D (2004)

Release Date

2004-07-20

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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