SMTL ID : 5onj.1

YnDL in Complex with 5 amino acid (PGA) complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x GLU- GGL- GGL- GGL- GGL- GGL: (2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYLOXY)-5-AMINO-2-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-3,4-DIOL(Non-covalent)

GLU-GGL-GGL-GGL-GGL-GGL.1: 31 residues within 4Å: Chain A: H.41, G.44, I.45, E.46, G.47, S.70, A.71, G.72, N.73, S.74, H.77, T.79, S.80, T.81, H.102, G.103, Y.104, A.105, H.144, A.145, G.146, V.147, S.148, N.151, Q.163, E.165, T.168, R.171, S.179, L.180 Ligands: ZN.2 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:E.46, A:T.81, A:H.144 Hydrogen bonds: A:I.45, A:I.45, A:E.46, A:G.47, A:S.70, A:G.72, A:N.73, A:N.73, A:S.74, A:S.80, A:H.102, A:G.103, A:A.105, A:H.144, A:G.146, A:V.147, A:S.148, A:N.151, A:Q.163, A:E.165, A:E.165, A:L.180 Water bridges: A:T.79, A:A.145, A:K.181, A:R.183 Salt bridges: A:H.41, A:H.77, A:H.102, A:R.171

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.41, E.46, H.102 Ligands: GLU-GGL-GGL-GGL-GGL-GGL.1, GLU-GGL-GGL-GGL-GGL-GGL.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.41, A:E.46, A:E.46, A:H.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ramaswamy, S. et al., The structure of PghL hydrolase bound to its substrate poly-gamma-glutamate. Febs J. (2018)

Release Date

2018-08-29

Peptides

YndL: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

YndL

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