SMTL ID : 7e6a.1

Crystal structure of cysteine desulfurase SufS C361A from Bacillus subtilis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: N.49, Q.50 Chain B: P.14, Q.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.14 EDO.2: 5 residues within 4Å: Chain A: H.307, A.311, E.329, E.330, R.331 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.331 EDO.3: 4 residues within 4Å: Chain A: R.78, N.82, A.83, Q.214 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.78, A:R.78, A:Q.214, A:Q.214 EDO.4: 3 residues within 4Å: Chain A: F.293, E.296, I.297 No protein-ligand interaction detected (PLIP) EDO.13: 4 residues within 4Å: Chain A: P.14, Q.18 Chain B: N.49, Q.50 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.14 EDO.14: 5 residues within 4Å: Chain B: H.307, A.311, E.329, E.330, R.331 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.331 EDO.15: 4 residues within 4Å: Chain B: R.78, N.82, A.83, Q.214 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.78, B:R.78, B:Q.214, B:Q.214 EDO.16: 3 residues within 4Å: Chain B: F.293, E.296, I.297 No protein-ligand interaction detected (PLIP)

14 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 5 residues within 4Å: Chain A: T.7, R.10, T.387, E.389, E.390 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.7, A:T.387, A:T.387, A:E.389 PEG.6: 5 residues within 4Å: Chain A: D.68, E.71, G.72, E.75, M.86 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.75, A:K.79 PEG.7: 4 residues within 4Å: Chain A: A.39, E.42, T.43, K.46 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.43 Water bridges: A:E.42 PEG.8: 4 residues within 4Å: Chain A: S.85, M.86, K.241, W.272 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.241, A:K.241 PEG.9: 3 residues within 4Å: Chain A: K.46, Q.50, Y.51 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.50 Water bridges: A:R.65 PEG.10: 5 residues within 4Å: Chain A: V.350, E.354, K.400, T.401, Y.404 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.354 PEG.11: 3 residues within 4Å: Chain A: P.14, H.17, R.38 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.17, A:R.38, A:R.38 PEG.17: 5 residues within 4Å: Chain B: T.7, R.10, T.387, E.389, E.390 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.7, B:T.387 PEG.18: 5 residues within 4Å: Chain B: D.68, E.71, G.72, E.75, M.86 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.75, B:K.79 PEG.19: 4 residues within 4Å: Chain B: A.39, E.42, T.43, K.46 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.42 PEG.20: 4 residues within 4Å: Chain B: S.85, M.86, K.241, W.272 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.241, B:K.241 PEG.21: 3 residues within 4Å: Chain B: K.46, Q.50, Y.51 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.50 Water bridges: B:R.65 PEG.22: 5 residues within 4Å: Chain B: V.350, E.354, K.400, T.401, Y.404 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.354 PEG.23: 3 residues within 4Å: Chain B: P.14, H.17, R.38 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.38, B:R.38

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.12: 5 residues within 4Å: Chain A: H.56, E.255, I.257, K.268, W.272 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.257, A:K.268 PG4.24: 5 residues within 4Å: Chain B: H.56, E.255, I.257, K.268, W.272 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.257, B:K.268 Water bridges: B:D.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamura, R. et al., Cycloserine enantiomers inhibit PLP-dependent cysteine desulfurase SufS via distinct mechanisms. Febs J. (2022)

Release Date

2022-03-02

Peptides

Cysteine desulfurase SufS: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cysteine desulfurase SufS

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