SMTL ID : 1m68.1

YCDX PROTEIN, TRINUCLEAR ZINC SITE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.15, H.40, H.194 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.15, A:H.40, A:H.194, H2O.1 ZN.2: 5 residues within 4Å: Chain A: H.7, H.9, E.73, D.192 Ligands: ZN.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.7, A:H.9, A:E.73, A:D.192, H2O.6 ZN.3: 4 residues within 4Å: Chain A: E.73, H.101, H.131 Ligands: ZN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.73, A:H.101, A:H.131, H2O.6 ZN.6: 3 residues within 4Å: Chain B: H.15, H.40, H.194 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.15, B:H.40, B:H.194, H2O.8 ZN.7: 5 residues within 4Å: Chain B: H.7, H.9, E.73, D.192 Ligands: ZN.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.7, B:H.9, B:E.73, B:D.192, H2O.13 ZN.8: 4 residues within 4Å: Chain B: E.73, H.101, H.131 Ligands: ZN.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.73, B:H.101, B:H.131, H2O.13 ZN.11: 3 residues within 4Å: Chain C: H.15, H.40, H.194 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.15, C:H.40, C:H.194, H2O.16 ZN.12: 5 residues within 4Å: Chain C: H.7, H.9, E.73, D.192 Ligands: ZN.13 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.7, C:H.9, C:E.73, C:D.192, H2O.20 ZN.13: 4 residues within 4Å: Chain C: E.73, H.101, H.131 Ligands: ZN.12 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.73, C:H.101, C:H.131, H2O.20

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: H.15 Chain C: I.54, N.55, R.57 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.57 Salt bridges: A:H.15 SO4.5: 5 residues within 4Å: Chain A: Y.2, L.209, F.214, P.216, I.219 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.2 SO4.9: 4 residues within 4Å: Chain A: I.54, N.55, R.57 Chain B: H.15 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.57 Salt bridges: B:H.15 SO4.10: 5 residues within 4Å: Chain B: Y.2, L.209, F.214, P.216, I.219 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.2 SO4.14: 4 residues within 4Å: Chain B: I.54, N.55, R.57 Chain C: H.15 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Salt bridges: C:H.15 Hydrogen bonds: B:R.57 SO4.15: 5 residues within 4Å: Chain C: Y.2, L.209, F.214, P.216, I.219 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Teplyakov, A. et al., Crystal structure of the Escherichia coli YcdX protein reveals atrinuclear zinc active site. PROTEINS: STRUCT.,FUNCT.,GENET. (2003)

Release Date

2003-04-22

Peptides

Hypothetical protein ycdX: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Hypothetical protein ycdX

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