SMTL ID : 3s2n.1

Crystal structure of dipeptidase from Streptomyces coelicolor complexed with phosphinate pseudodipeptide L-Tyr-D-Asp

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x P4D: (2R)-2-{[(S)-[(1R)-1-amino-2-(4-hydroxyphenyl)ethyl](hydroxy)phosphoryl]methyl}butanedioic acid(Non-covalent)

P4D.1: 17 residues within 4Å: Chain A: H.20, D.22, W.25, Y.68, E.123, H.150, H.191, H.212, R.223, K.247, F.248, D.320, G.323, T.324, P.325 Ligands: ZN.2, ZN.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.68 Hydrogen bonds: A:D.22, A:T.324, A:T.324 Water bridges: A:N.151, A:N.151, A:H.191, A:K.247, A:K.247 Salt bridges: A:H.191, A:H.212, A:R.223, A:K.247

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: H.20, D.22, S.66, E.123, D.320 Ligands: P4D.1, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.20, A:D.22, A:D.22, A:E.123 ZN.3: 6 residues within 4Å: Chain A: E.123, H.191, H.212, R.223 Ligands: P4D.1, ZN.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.123, A:H.191, A:H.212

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 6 residues within 4Å: Chain A: H.126, D.129, N.130, N.154, A.155, W.156 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:H.126, A:D.129, A:N.130, A:N.130, A:A.155 Water bridges: A:D.129, A:D.129, A:D.129 EDO.5: 2 residues within 4Å: Chain A: D.367, R.374 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.374 Water bridges: A:R.374 EDO.6: 6 residues within 4Å: Chain A: V.218, V.249, L.250, Q.251, T.298, D.301 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.251, A:D.301, A:D.301 Water bridges: A:A.252 EDO.7: 5 residues within 4Å: Chain A: S.234, G.237, D.313, H.314, R.364 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.234, A:D.313 EDO.8: 3 residues within 4Å: Chain A: P.207, R.364, A.368 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.237, A:D.367 EDO.9: 5 residues within 4Å: Chain A: S.45, A.46, H.47, L.48, H.49 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.46, A:H.49 EDO.10: 3 residues within 4Å: Chain A: I.84, D.85, R.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fedorov, A.A. et al., Crystal structure of dipeptidase from Streptomyces coelicolor complexed with phosphinate pseudodipeptide L-Tyr-D-Asp. To be Published

Release Date

2011-06-22

Peptides

dipeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

dipeptidase

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