SMTL ID : 7e6b.1

Crystal structure of PMP-bound form of cysteine desulfurase SufS C361A from Bacillus subtilis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 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, V.174, N.176, D.201, A.203, S.224, H.226, K.227 Chain B: G.277, T.278 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.203 Hydrogen bonds: A:T.95, 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.96, A:T.97, A:R.359, 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, V.174, N.176, D.201, A.203, S.224, H.226, K.227 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.203 Hydrogen bonds: B:T.95, 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, A:T.278 Salt bridges: B:H.226 pi-Stacking: B:H.124

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

EDO.2: 6 residues within 4Å: Chain A: H.307, A.310, 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: L.16, H.17, Q.18, D.24 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.17 EDO.4: 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.14: 6 residues within 4Å: Chain B: H.307, A.310, A.311, E.329, E.330, R.331 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.330, B:R.331 EDO.15: 4 residues within 4Å: Chain B: L.16, H.17, Q.18, D.24 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.17 EDO.16: 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

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

PEG.5: 3 residues within 4Å: Chain A: V.181, S.303, R.331 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.303 Water bridges: A:K.210 PEG.6: 5 residues within 4Å: Chain A: T.7, R.10, T.387, E.389, E.390 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.387, A:T.387 Water bridges: A:R.10 PEG.7: 4 residues within 4Å: Chain A: P.14, 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.8: 5 residues within 4Å: Chain A: D.68, E.71, G.72, E.75, M.86 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.68 PEG.9: 4 residues within 4Å: Chain A: V.350, E.354, K.400, Y.404 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.354 PEG.10: 4 residues within 4Å: Chain A: K.46, Q.50, Y.51, R.65 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.46, A:Q.50 Water bridges: A:R.65 PEG.11: 4 residues within 4Å: Chain A: D.8, F.293, E.296, I.297 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.8, A:Q.12 PEG.17: 3 residues within 4Å: Chain B: V.181, S.303, R.331 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.303 Water bridges: B:K.210 PEG.18: 5 residues within 4Å: Chain B: T.7, R.10, T.387, E.389, E.390 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.7, B:T.387 Water bridges: B:R.10 PEG.19: 4 residues within 4Å: Chain A: N.49, Q.50 Chain B: P.14, Q.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.50 Water bridges: A:N.49 PEG.20: 5 residues within 4Å: Chain B: D.68, E.71, G.72, E.75, M.86 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.68 PEG.21: 4 residues within 4Å: Chain B: V.350, E.354, K.400, Y.404 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.354 PEG.22: 4 residues within 4Å: Chain B: K.46, Q.50, Y.51, R.65 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.46, B:Q.50 Water bridges: B:R.65 PEG.23: 4 residues within 4Å: Chain B: D.8, F.293, E.296, I.297 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.8, B:Q.12

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

PG4.12: 5 residues within 4Å: Chain A: H.56, E.255, K.268, E.269, W.272 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.268 PG4.24: 5 residues within 4Å: Chain B: H.56, E.255, K.268, E.269, W.272 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.268, B:E.269

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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