SMTL ID : 1sbr.1

The structure and function of B. subtilis YkoF gene product: the complex with thiamin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: A.33, T.35 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.33, A:T.35, H2O.1

4 x VIB: 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM(Non-covalent)

VIB.2: 12 residues within 4Å: Chain A: F.15, S.16, L.17, I.25, I.28, K.29, T.44, D.45, H.46, I.47, S.48, T.49 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.15, A:L.17, A:T.44 Hydrogen bonds: A:L.17, A:L.17 VIB.3: 10 residues within 4Å: Chain A: F.119, A.120, L.121, Y.129, M.130, I.133, Y.152, A.153, S.154 Chain B: C.86 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.119, A:L.121 Hydrogen bonds: A:L.121, A:L.121 VIB.4: 12 residues within 4Å: Chain B: F.15, S.16, L.17, I.25, I.28, K.29, T.44, D.45, H.46, I.47, S.48, T.49 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.15, B:T.44 Hydrogen bonds: B:L.17, B:L.17, B:T.49 VIB.5: 11 residues within 4Å: Chain A: P.87, H.180 Chain B: F.119, A.120, L.121, Y.129, M.130, I.133, Y.152, A.153, S.154 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.119, B:I.133 Hydrogen bonds: B:L.121, B:L.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Devedjiev, Y. et al., The Structure and Ligand Binding Properties of the B.subtilis YkoF Gene Product, a Member of a Novel Family of Thiamin/HMP-binding Proteins. J.Mol.Biol. (2004)

Release Date

2004-10-05

Peptides

ykoF: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ykoF

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