SMTL ID : 7cep.1

Crystal structure of L-cycloserine-bound form of cysteine desulfurase SufS from Bacillus subtilis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

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

PEG.1: 4 residues within 4Å: Chain A: H.56, E.255, K.268, W.272 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.255, A:E.255, A:K.268 PEG.2: 6 residues within 4Å: Chain A: D.8, Q.12, F.293, E.296, I.297 Ligands: PEG.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.12 Water bridges: A:E.296 PEG.3: 5 residues within 4Å: Chain A: P.14, H.17, Q.18 Chain B: N.49, Q.50 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.50 Water bridges: B:N.49 PEG.4: 6 residues within 4Å: Chain A: V.181, M.209, S.303, R.304, E.330, R.331 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.303, A:R.304, A:R.331 Water bridges: A:K.210, A:K.210, A:R.304 PEG.5: 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.6: 4 residues within 4Å: Chain A: A.39, E.42, T.43 Ligands: PEG.2 No protein-ligand interaction detected (PLIP) PEG.9: 4 residues within 4Å: Chain B: H.56, E.255, K.268, W.272 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.255, B:K.268 PEG.10: 6 residues within 4Å: Chain B: D.8, Q.12, F.293, E.296, I.297 Ligands: PEG.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.12 Water bridges: B:E.296, B:E.296 PEG.11: 5 residues within 4Å: Chain A: N.49, Q.50 Chain B: P.14, H.17, Q.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.50 Water bridges: A:N.49 PEG.12: 6 residues within 4Å: Chain B: V.181, M.209, S.303, R.304, E.330, R.331 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.303, B:R.304, B:E.330, B:R.331 Water bridges: B:K.210, B:K.210, B:R.304 PEG.13: 5 residues within 4Å: Chain B: V.350, E.354, K.400, T.401, Y.404 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.354 Water bridges: B:E.354 PEG.14: 4 residues within 4Å: Chain B: A.39, E.42, T.43 Ligands: PEG.10 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.296

2 x 7TS: (5-hydroxy-6-methyl-4-{[(3-oxo-2,3-dihydro-1,2-oxazol-4-yl)amino]methyl}pyridin-3-yl)methyl dihydrogen phosphate(Non-covalent)

7TS.7: 16 residues within 4Å: Chain A: A.31, A.32, T.95, T.96, H.124, A.126, N.176, D.201, A.203, S.224, H.226, K.227, R.379 Chain B: N.54, G.277, T.278 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.203 Hydrogen bonds: A:T.96, A:N.176, A:S.224, A:S.224, A:K.227, A:R.379, A:R.379, B:T.278, B:T.278, B:T.278 Water bridges: A:T.97 Salt bridges: A:H.226 pi-Stacking: A:H.124 7TS.15: 16 residues within 4Å: Chain A: N.54, G.277, T.278 Chain B: A.31, A.32, T.95, T.96, H.124, A.126, N.176, D.201, A.203, S.224, H.226, K.227, R.379 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.203 Hydrogen bonds: B:T.96, B:T.96, B:N.176, B:S.224, B:S.224, B:K.227, B:R.379, B:R.379, A:T.278, A:T.278 Water bridges: B:T.97 Salt bridges: B:H.226 pi-Stacking: B:H.124

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.8: 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.387, A:T.387, A:E.389 Water bridges: A:E.388 PGE.16: 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.387 Water bridges: B:E.388

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

2021-06-30

Peptides

Cysteine desulfurase SufS: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cysteine desulfurase SufS

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