SMTL ID : 1rxq.1 (2 other biounits)

YfiT from Bacillus subtilis is a probable metal-dependent hydrolase with an unusual four-helix bundle topology

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 3 residues within 4Å: Chain A: H.67, H.160, H.164 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.67, A:H.164, H2O.1, H2O.1, H2O.1 NI.2: 3 residues within 4Å: Chain B: H.67, H.160, H.164 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.67, B:H.160, B:H.164, H2O.5, H2O.5, H2O.5 NI.3: 3 residues within 4Å: Chain C: H.67, H.160, H.164 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.67, C:H.160, C:H.164, H2O.9, H2O.9, H2O.11 NI.4: 4 residues within 4Å: Chain D: H.67, H.160, H.164 Ligands: GLU.5 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.67, D:H.160, D:H.164, H2O.18, H2O.18, H2O.18

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.5: 10 residues within 4Å: Chain D: W.59, H.67, E.95, W.159, H.160, H.164 Ligands: NI.4, SER.6, ALA.7, THR.8 7 PLIP interactions: 2 Ligand-Ligand interactions, 5 interactions with chain D Hydrogen bonds: A.7, T.8 Water bridges: D:E.95, D:E.95 Salt bridges: D:H.67, D:H.160, D:H.164

2 x SER: SERINE(Non-covalent)

SER.6: 7 residues within 4Å: Chain D: L.156, Y.157, W.159, H.160 Ligands: GLU.5, ALA.7, THR.8 4 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain D Hydrogen bonds: A.7, D:Y.157 Water bridges: D:E.95, D:E.95 SER.9: 3 residues within 4Å: Chain D: E.12 Ligands: THR.8, GLY.10 4 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain D Water bridges: S.9, S.9 Hydrogen bonds: D:E.12, D:E.12

1 x ALA: ALANINE(Non-covalent)

ALA.7: 4 residues within 4Å: Chain D: L.156 Ligands: GLU.5, SER.6, THR.8 4 PLIP interactions: 3 Ligand-Ligand interactions, 1 interactions with chain D Hydrogen bonds: E.5, E.5, T.8 Hydrophobic interactions: D:L.156

1 x THR: THREONINE(Non-functional Binders)

THR.8: 5 residues within 4Å: Ligands: GLU.5, SER.6, ALA.7, SER.9, GLY.10 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: E.5, G.10

1 x GLY: GLYCINE(Non-functional Binders)

GLY.10: 2 residues within 4Å: Ligands: THR.8, SER.9 1 PLIP interactions: 1 Ligand-Ligand interactions Hydrogen bonds: T.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rajan, S.S. et al., YfiT from Bacillus subtilis Is a Probable Metal-Dependent Hydrolase with an Unusual Four-Helix Bundle Topology. Biochemistry (2004)

Release Date

2004-07-20

Peptides

yfiT: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

yfiT

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