SMTL ID : 7ysl.1

Crystal structure of D-Cysteine desulfhydrase with a trapped PLP-pyruvate geminal diamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-dimer

Ligands

12 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 5 residues within 4Å: Chain A: E.262, R.284, S.285, V.287, R.288 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.258, A:R.284, A:S.285 FMT.4: 2 residues within 4Å: Chain A: D.160, A.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.160, A:A.171 FMT.5: 3 residues within 4Å: Chain A: R.39, F.40, P.41 No protein-ligand interaction detected (PLIP) FMT.6: 3 residues within 4Å: Chain A: Y.61, L.62, R.337 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.61, A:Y.61, A:R.337 FMT.8: 4 residues within 4Å: Chain A: P.301, E.303, L.306, L.364 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.301 FMT.9: 1 residues within 4Å: Chain A: R.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.134 FMT.10: 3 residues within 4Å: Chain A: R.144, V.148, N.152 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.144, A:N.152 FMT.11: 5 residues within 4Å: Chain A: S.44, L.45, H.47, K.122 Chain B: E.53 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:E.53, B:R.71 Hydrogen bonds: A:K.122, A:K.122 FMT.12: 3 residues within 4Å: Chain B: G.124, L.125, K.126 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.125 Water bridges: B:G.124 FMT.13: 4 residues within 4Å: Chain B: S.59, G.64, P.65, T.66 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.66 FMT.14: 3 residues within 4Å: Chain B: P.186, Y.187, V.188 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.188 FMT.15: 3 residues within 4Å: Chain B: Y.138, Q.363, Q.367 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.367

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

EDO.2: 2 residues within 4Å: Chain A: R.39, F.40 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.39, A:R.39 EDO.3: 4 residues within 4Å: Chain A: E.307, R.310, Q.314 Ligands: EDO.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.310, A:Q.314 Water bridges: A:E.307, A:E.307 EDO.7: 2 residues within 4Å: Chain A: L.315 Ligands: EDO.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, X. et al., Characterization and structural basis of D-cysteine desulfhydrase from Pectobacterium atrosepticum. Tetrahedron (2022)

Release Date

2022-12-14

Peptides

D-Cysteine desulfhydrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-Cysteine desulfhydrase

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