SMTL ID : 7e6e.1

Crystal structure of PMP-bound form of cysteine desulfurase SufS R376A from Bacillus subtilis in D-cycloserine-inhibition

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-dimer

Ligands

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

PMP.1: 14 residues within 4Å: Chain A: A.31, T.95, T.96, H.124, A.126, N.176, D.201, A.203, Q.204, S.224, H.226, K.227 Chain B: G.277, T.278 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.203, A:Q.204 Hydrogen bonds: A:T.96, A:T.96, A:T.96, A:S.224, A:K.227, A:K.227, B:T.278, B:T.278, B:T.278 Water bridges: A:T.97, A:R.359 Salt bridges: A:H.226 pi-Stacking: A:H.124 PMP.13: 14 residues within 4Å: Chain A: G.277, T.278 Chain B: A.31, T.95, T.96, H.124, A.126, N.176, D.201, A.203, Q.204, S.224, H.226, K.227 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.203, B:Q.204 Hydrogen bonds: B:T.96, B:T.96, B:T.96, B:S.224, B:K.227, B:K.227, A:T.278, A:T.278 Water bridges: B:T.97, B:R.359 Salt bridges: B:H.226 pi-Stacking: B:H.124

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

PG4.2: 5 residues within 4Å: Chain A: H.56, E.255, K.268, W.272 Chain B: H.362 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.268, B:H.362 PG4.14: 5 residues within 4Å: Chain A: H.362 Chain B: H.56, E.255, K.268, W.272 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.268, A:H.362

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

PEG.3: 3 residues within 4Å: Chain A: E.71, M.86, W.272 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.71, A:E.71, A:S.85, A:S.85 PEG.4: 4 residues within 4Å: Chain A: V.181, S.303, H.307, R.331 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.303 Water bridges: A:D.300, A:S.303 PEG.5: 6 residues within 4Å: Chain A: H.56, R.57, G.58, T.67, E.71, W.272 No protein-ligand interaction detected (PLIP) PEG.6: 4 residues within 4Å: Chain A: N.49, Q.50 Chain B: P.14, Q.18 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.18, A:Q.50 Water bridges: A:N.49 PEG.15: 3 residues within 4Å: Chain B: E.71, M.86, W.272 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.71, B:S.85, B:S.85 PEG.16: 4 residues within 4Å: Chain B: V.181, S.303, H.307, R.331 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.303 Water bridges: B:D.300, B:D.300 PEG.17: 6 residues within 4Å: Chain B: H.56, R.57, G.58, T.67, E.71, W.272 No protein-ligand interaction detected (PLIP) PEG.18: 4 residues within 4Å: Chain A: P.14, Q.18 Chain B: N.49, Q.50 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.50, A:Q.18 Water bridges: B:N.49

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

EDO.7: 2 residues within 4Å: Chain A: G.72, E.75 No protein-ligand interaction detected (PLIP) EDO.8: 3 residues within 4Å: Chain A: R.10, T.387, E.389 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.387, A:T.387 EDO.9: 4 residues within 4Å: Chain A: L.16, H.17, Q.18, D.24 No protein-ligand interaction detected (PLIP) EDO.10: 2 residues within 4Å: Chain A: D.8, I.297 No protein-ligand interaction detected (PLIP) EDO.11: 2 residues within 4Å: Chain A: A.39, T.43 No protein-ligand interaction detected (PLIP) EDO.12: 2 residues within 4Å: Chain A: R.316, Q.319 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.316 Water bridges: A:R.316 EDO.19: 2 residues within 4Å: Chain B: G.72, E.75 No protein-ligand interaction detected (PLIP) EDO.20: 3 residues within 4Å: Chain B: R.10, T.387, E.389 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.387 EDO.21: 4 residues within 4Å: Chain B: L.16, H.17, Q.18, D.24 No protein-ligand interaction detected (PLIP) EDO.22: 2 residues within 4Å: Chain B: D.8, I.297 No protein-ligand interaction detected (PLIP) EDO.23: 2 residues within 4Å: Chain B: A.39, T.43 No protein-ligand interaction detected (PLIP) EDO.24: 2 residues within 4Å: Chain B: R.316, Q.319 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.316 Water bridges: B:R.316

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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