SMTL ID : 3tlq.1 (1 other biounit)

Crystal structure of EAL-like domain protein YdiV

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

monomer

Ligands

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 5 residues within 4Å: Chain A: D.17, H.38, F.39, S.40, R.47 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.17, A:D.17, A:H.38 Water bridges: A:R.47 Salt bridges: A:R.47 PO4.2: 4 residues within 4Å: Chain A: T.37, H.38, T.50 Ligands: GOL.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.37, A:T.50 Water bridges: A:T.50, A:T.50 Salt bridges: A:H.38 PO4.3: 6 residues within 4Å: Chain A: F.9, L.10, N.12, L.13, Q.61, Q.64 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.12, A:Q.61, A:Q.64, A:Q.64 PO4.4: 2 residues within 4Å: Chain A: Q.241, R.242 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.241, A:R.242, A:R.242 Salt bridges: A:R.242 PO4.5: 3 residues within 4Å: Chain A: H.83, V.240, Q.241 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.241 Salt bridges: A:H.83

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: H.125, N.127, E.128 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.127, A:E.128 Water bridges: A:H.125, A:H.125, A:L.126 GOL.7: 7 residues within 4Å: Chain A: L.35, I.36, T.37, L.65, Q.69, N.90 Ligands: PO4.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.37, A:T.37, A:T.50, A:Q.69 Water bridges: A:Q.69 GOL.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, B. et al., Structural insight of a concentration-dependent mechanism by which YdiV inhibits Escherichia coli flagellum biogenesis and motility. Nucleic Acids Res. (2012)

Release Date

2012-09-12

Peptides

Regulatory protein YdiV: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Regulatory protein YdiV

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