SMTL ID : 7uf3.1

RibB from Vibrio cholera bound with L-xylulose-5-phosphate (L-Xy5P) and manganese

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x N3U: L-xylulose-5-phosphate(Non-covalent)

N3U.1: 18 residues within 4Å: Chain A: R.38, E.39, D.43, C.68, N.92, T.94, F.96, L.141, R.151, G.153, H.154, T.155, L.173, C.174, E.175 Chain B: H.137 Ligands: MN.2, MN.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.43, A:T.94, A:T.94, A:H.154, A:T.155, A:T.155, A:T.155, A:E.175 Water bridges: A:E.41, A:N.92 Salt bridges: A:R.38, A:R.151 N3U.5: 18 residues within 4Å: Chain A: H.137 Chain B: R.38, E.39, D.43, C.68, N.92, T.94, F.96, L.141, R.151, G.153, H.154, T.155, L.173, C.174, E.175 Ligands: MN.6, MN.7 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.43, B:T.94, B:T.94, B:H.154, B:T.155, B:T.155, B:T.155, B:E.175, B:E.175 Water bridges: B:N.92 Salt bridges: B:R.38, B:R.151

6 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.2: 6 residues within 4Å: Chain A: R.38, E.39, D.43, H.154 Ligands: N3U.1, MN.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.39, A:H.154, H2O.2 MN.3: 7 residues within 4Å: Chain A: E.39, N.92, T.94 Chain B: T.108, H.137 Ligands: N3U.1, MN.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.39, H2O.2, H2O.2, H2O.6 MN.4: 3 residues within 4Å: Chain A: L.149, I.211, D.214 No protein-ligand interaction detected (PLIP) MN.6: 6 residues within 4Å: Chain B: R.38, E.39, D.43, H.154 Ligands: N3U.5, MN.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.39, B:H.154, H2O.6 MN.7: 7 residues within 4Å: Chain A: T.108, H.137 Chain B: E.39, N.92, T.94 Ligands: N3U.5, MN.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.39, H2O.1, H2O.6, H2O.7 MN.8: 3 residues within 4Å: Chain B: L.149, I.211, D.214 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kenjic, N. et al., Evidence for the Chemical Mechanism of RibB (3,4-Dihydroxy-2-butanone 4-phosphate Synthase) of Riboflavin Biosynthesis. J.Am.Chem.Soc. (2022)

Release Date

2022-07-20

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

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

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