SMTL ID : 4d9b.2 (1 other biounit)

Pyridoxamine 5' phosphate (PMP) bound form of Salmonella typhimurium D-Cysteine desulfhydrase obtained after co-crystallization with D-cycloserine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-dimer

Ligands

2 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.1: 3 residues within 4Å: Chain A: Y.44, L.45, S.314 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.44 Hydrogen bonds: A:L.45, A:S.314 BEN.4: 4 residues within 4Å: Chain B: Y.44, L.45, I.310, I.313 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.44, B:L.45, B:I.310, B:I.313 Hydrogen bonds: B:Y.44

2 x PMP: 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PMP.2: 16 residues within 4Å: Chain A: N.64, K.65, K.68, N.93, S.175, A.206, S.207, G.208, S.209, A.210, G.211, T.212, Y.301, T.329, G.330, G.331 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.301 Hydrogen bonds: A:N.64, A:N.93, A:S.175, A:G.208, A:S.209, A:A.210, A:T.212, A:T.212, A:T.329 Water bridges: A:N.93, A:H.94, A:S.209, A:H.213, A:Y.301, A:Y.301 Salt bridges: A:K.65, A:K.68 pi-Stacking: A:Y.301 PMP.5: 16 residues within 4Å: Chain B: N.64, K.65, K.68, N.93, S.175, A.206, S.207, G.208, S.209, A.210, G.211, T.212, Y.301, T.329, G.330, G.331 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:Y.301 Hydrogen bonds: B:N.64, B:N.93, B:S.175, B:G.208, B:S.209, B:A.210, B:G.211, B:T.212, B:T.212, B:T.212 Water bridges: B:S.209, B:H.213, B:Y.275, B:Y.275, B:Y.301, B:Y.301, B:Y.301 Salt bridges: B:K.65, B:K.68 pi-Stacking: B:Y.301

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

EDO.3: 5 residues within 4Å: Chain A: G.208, S.209, S.235, R.236, Y.275 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.235, A:S.235, A:R.236, A:R.236 EDO.6: 4 residues within 4Å: Chain B: G.208, S.209, S.235, R.236 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.235, B:S.235, B:R.236, B:R.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bharath, S.R. et al., Structural and Mutational Studies on Substrate Specificity and Catalysis of Salmonella typhimurium D-Cysteine Desulfhydrase. Plos One (2012)

Release Date

2012-05-30

Peptides

D-cysteine desulfhydrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

D-cysteine desulfhydrase

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