SMTL ID : 1pb0.1

YCDX PROTEIN IN AUTOINHIBITED STATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-trimer

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.15, H.40, H.164, H.194 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.15, A:H.40, A:H.164, A:H.194 ZN.2: 6 residues within 4Å: Chain A: H.7, H.9, H.40, 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.1 ZN.3: 4 residues within 4Å: Chain A: E.73, H.101, H.131 Ligands: ZN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.73, A:E.73, A:H.101, A:H.131, H2O.1 ZN.7: 4 residues within 4Å: Chain B: H.15, H.40, H.164, H.194 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.15, B:H.40, B:H.164, B:H.194 ZN.8: 6 residues within 4Å: Chain B: H.7, H.9, H.40, E.73, D.192 Ligands: ZN.9 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.9: 4 residues within 4Å: Chain B: E.73, H.101, H.131 Ligands: ZN.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.73, B:E.73, B:H.101, B:H.131, H2O.13 ZN.14: 4 residues within 4Å: Chain C: H.15, H.40, H.164, H.194 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.15, C:H.40, C:H.164, C:H.194 ZN.15: 6 residues within 4Å: Chain C: H.7, H.9, H.40, E.73, D.192 Ligands: ZN.16 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.18 ZN.16: 4 residues within 4Å: Chain C: E.73, H.101, H.131 Ligands: ZN.15 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.73, C:E.73, C:H.101, C:H.131, H2O.18

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

SO4.4: 3 residues within 4Å: Chain A: Q.152, W.186, R.218 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.152 Water bridges: A:W.186, A:R.218 Salt bridges: A:R.218 SO4.5: 2 residues within 4Å: Chain A: R.57, R.70 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.61, A:R.61, A:R.61, A:R.70 Salt bridges: A:R.61, A:R.70 SO4.10: 3 residues within 4Å: Chain B: Q.152, W.186, R.218 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.152 Water bridges: B:W.186, B:R.218, B:S.233 Salt bridges: B:R.218 SO4.17: 3 residues within 4Å: Chain C: Q.152, W.186, R.218 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.152 Water bridges: C:R.218 Salt bridges: C:R.218

6 x FMT: FORMIC ACID(Non-functional Binders)

FMT.6: 3 residues within 4Å: Chain A: P.60, R.61, V.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.61, A:V.62 FMT.11: 3 residues within 4Å: Chain B: P.60, R.61, V.62 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.61, B:V.62 FMT.12: 3 residues within 4Å: Chain B: A.178, R.181, V.212 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.181, B:R.181 FMT.13: 1 residues within 4Å: Chain B: R.70 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.70, B:R.70 Water bridges: B:R.61, B:R.61, B:R.61 FMT.18: 3 residues within 4Å: Chain C: P.60, R.61, V.62 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.61, C:V.62 FMT.19: 2 residues within 4Å: Chain C: R.181, V.212 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.181, C:R.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Teplyakov, A. et al., Autoregulation of YcdX protein. To be Published

Release Date

2004-05-25

Peptides

Hypothetical protein ycdX: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Hypothetical protein ycdX

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