SMTL ID : 7cet.1

Crystal structure of D-cycloserine-bound form of cysteine desulfurase NifS from Helicobacter pylori

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.64 Å

Oligo State

homo-dimer

Ligands

2 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.1: 7 residues within 4Å: Chain A: L.52, Y.56, D.66, V.67, I.68, M.234, N.235 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.52, A:Y.56 Hydrogen bonds: A:D.66, A:D.66, A:V.67 IPA.4: 7 residues within 4Å: Chain B: L.52, Y.56, D.66, V.67, I.68, M.234, N.235 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.52, B:Y.56 Hydrogen bonds: B:Y.56, B:D.66, B:V.67

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: P.226, L.227 Chain B: K.82 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: K.82 Chain B: P.226, L.227 Ligand excluded by PLIP

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.3: 16 residues within 4Å: Chain A: N.10, A.11, C.72, A.73, T.74, H.104, N.155, D.180, V.182, Q.183, S.203, H.205, K.206 Chain B: E.232, G.240, T.241 14 PLIP interactions: 4 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:T.241, B:T.241, A:A.73, A:T.74, A:T.74, A:H.104, A:Q.183, A:S.203 Water bridges: B:N.33, B:E.232 Hydrophobic interactions: A:V.182, A:V.182 Salt bridges: A:H.205 pi-Stacking: A:H.104 7TS.6: 16 residues within 4Å: Chain A: E.232, G.240, T.241 Chain B: N.10, A.11, C.72, A.73, T.74, H.104, N.155, D.180, V.182, Q.183, S.203, H.205, K.206 13 PLIP interactions: 4 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:T.241, A:T.241, A:T.241, B:A.73, B:T.74, B:H.104, B:Q.183, B:S.203 Water bridges: A:N.33 Hydrophobic interactions: B:V.182, B:V.182 Salt bridges: B:H.205 pi-Stacking: B:H.104

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 IscS: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cysteine desulfurase IscS

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