SMTL ID : 7z6f.1

Crystal structure of the substrate-binding protein YejA in complex with peptide fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-1-1-mer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: W.317, G.378, P.429, H.432, R.436 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.436 Water bridges: A:P.429, A:H.432 GOL.2: 6 residues within 4Å: Chain A: L.39, R.60, W.225, I.230, I.564, D.565 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.60, A:R.60 Water bridges: A:Q.63, A:Q.63, A:W.225, A:Y.232, A:D.565 GOL.3: 5 residues within 4Å: Chain A: P.130, R.456, N.487, T.489 Chain B: F.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.456 Water bridges: A:N.487 GOL.4: 6 residues within 4Å: Chain A: F.106, H.107, G.109, D.212, Y.213, W.214 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.214 Water bridges: A:F.106, A:H.107, A:D.212

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

CL.5: 4 residues within 4Å: Chain A: V.27, N.28, P.554, A.555 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain A: P.130, N.487 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beis, K. et al., Crystal structure of the substrate-binding protein YejA in complex with peptide fragment. To Be Published

Release Date

2023-09-20

Peptides

YejA: A
degradation peptide VAL-LEU-GLY-GLU-PRO-ARG-TYR-ALA-PHE-ASN-PHE-ASN: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
A

YejA

degradation peptide VAL-LEU-GLY-GLU-PRO-ARG-TYR-ALA-PHE-ASN-PHE-ASN