SMTL ID : 6ofu.1

X-ray crystal structure of the YdjI aldolase from Escherichia coli K12

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.82, H.178, H.206 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.82, A:H.178, A:H.206, H2O.2, H2O.6 ZN.3: 4 residues within 4Å: Chain B: H.82, E.133, H.178, H.206 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.82, B:E.133, B:H.178, B:H.206, H2O.15 ZN.5: 3 residues within 4Å: Chain C: H.82, H.206 Ligands: ZN.6 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.82, H2O.22, H2O.26, H2O.27 ZN.6: 5 residues within 4Å: Chain C: H.82, D.103, E.133, H.206 Ligands: ZN.5 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.133, C:E.133, C:H.206, H2O.21, H2O.28 ZN.7: 3 residues within 4Å: Chain D: H.82, E.133, H.206 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.82, D:E.133, D:H.206, H2O.31, H2O.37

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 1 residues within 4Å: Chain A: R.164 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain B: R.164 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huddleston, J.P. et al., Structural and Functional Characterization of YdjI, an Aldolase of Unknown Specificity inEscherichia coliK12. Biochemistry (2019)

Release Date

2019-04-24

Peptides

YdjI aldolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

YdjI aldolase