SMTL ID : 5fpz.1

The structure of KdgF from Yersinia enterocolitica with malonate bound in the active site.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

NI.1: 5 residues within 4Å: Chain A: H.46, H.48, Q.53, H.87 Ligands: MLA.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.46, A:H.48, A:H.87 NI.3: 5 residues within 4Å: Chain B: H.46, H.48, Q.53, H.87 Ligands: MLA.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.46, B:H.48, B:H.87

2 x MLA: MALONIC ACID(Non-covalent)

MLA.2: 9 residues within 4Å: Chain A: H.46, H.48, Q.53, H.87, D.100, F.102, R.106, F.109 Ligands: NI.1 11 PLIP interactions: 11 interactions with chain A Water bridges: A:R.21, A:R.21, A:D.100, A:D.100, A:R.106, A:R.106 Salt bridges: A:H.46, A:H.46, A:H.48, A:H.87, A:R.106 MLA.4: 9 residues within 4Å: Chain B: H.46, H.48, Q.53, H.87, D.100, F.102, R.106, F.109 Ligands: NI.3 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Q.53 Water bridges: B:R.21, B:R.21, B:Y.79, B:Y.79, B:D.100, B:R.106, B:R.106 Salt bridges: B:H.46, B:H.46, B:H.48, B:H.87, B:R.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hobbs, J.K. et al., Kdgf, the Missing Link in the Microbial Metabolism of Uronate Sugars from Pectin and Alginate. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-05-04

Peptides

PECTIN DEGRADATION PROTEIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PECTIN DEGRADATION PROTEIN