SMTL ID : 7ceo.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

homo-dimer

Ligands

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

PEG.1: 5 residues within 4Å: Chain A: H.56, E.255, K.268, E.269, W.272 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.255, A:E.255 PEG.2: 5 residues within 4Å: Chain A: I.9, Q.12, F.293, E.296, I.297 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.12 PEG.3: 4 residues within 4Å: Chain A: V.181, M.209, S.303, R.331 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.303, A:R.331 Water bridges: A:K.210 PEG.5: 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:E.255, B:E.269 PEG.6: 5 residues within 4Å: Chain B: I.9, Q.12, F.293, E.296, I.297 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.12 Water bridges: B:E.296 PEG.7: 4 residues within 4Å: Chain B: V.181, M.209, S.303, R.331 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.303, B:R.331 Water bridges: B:K.210

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

PMP.4: 14 residues within 4Å: Chain A: A.31, T.95, T.96, H.124, V.174, 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:N.176, A:A.203, A:Q.204 Hydrogen bonds: A:A.31, A:T.95, A:T.96, A:T.96, A:S.224, A:K.227, B:T.278, B:T.278, B:T.278 Water bridges: A:T.97 Salt bridges: A:H.226 pi-Stacking: A:H.124 PMP.8: 14 residues within 4Å: Chain A: G.277, T.278 Chain B: A.31, T.95, T.96, H.124, V.174, N.176, D.201, A.203, Q.204, S.224, H.226, K.227 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:N.176, B:A.203, B:Q.204 Hydrogen bonds: B:A.31, B:T.95, B:T.96, B:T.96, B:T.96, B:S.224, B:K.227, A:T.278, A:T.278 Water bridges: B:T.97 Salt bridges: B:H.226 pi-Stacking: B:H.124

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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