SMTL ID : 7xeq.1

NifS with D-cysteine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

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

IPA.1: 6 residues within 4Å: Chain A: L.52, Y.56, D.66, V.67, I.68, N.235 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.52, A:Y.56 Hydrogen bonds: A:D.66, A:V.67, A:N.235 IPA.4: 6 residues within 4Å: Chain B: L.52, Y.56, D.66, V.67, I.68, N.235 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.52, B:Y.56 Hydrogen bonds: B:Y.56, B:D.66, B:D.66, B:V.67, B:N.235

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

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

2 x 9YX: (2~{S},4~{S})-2-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]-1,3-thiazolidine-4-carboxylic acid(Non-covalent)

9YX.3: 16 residues within 4Å: Chain A: N.10, A.11, C.72, A.73, T.74, H.104, M.151, N.155, D.180, V.182, S.203, H.205, K.206, R.354 Chain B: G.240, T.241 19 PLIP interactions: 3 interactions with chain B, 16 interactions with chain A Hydrogen bonds: B:T.241, A:A.73, A:T.74, A:T.74, A:N.77, A:N.155, A:S.203, A:K.206, A:K.206 Water bridges: B:G.240, B:G.240, A:R.354 Hydrophobic interactions: A:H.104, A:V.182, A:V.182 Salt bridges: A:H.205, A:K.206, A:R.354 pi-Stacking: A:H.104 9YX.6: 16 residues within 4Å: Chain A: G.240, T.241 Chain B: N.10, A.11, C.72, A.73, T.74, H.104, M.151, N.155, D.180, V.182, S.203, H.205, K.206, R.354 20 PLIP interactions: 16 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:H.104, B:V.182, B:V.182 Hydrogen bonds: B:A.73, B:T.74, B:T.74, B:N.77, B:N.155, B:S.203, B:K.206, B:K.206, A:T.241, A:T.241 Water bridges: B:R.354, A:G.240, A:G.240 Salt bridges: B:H.205, B:K.206, B:R.354 pi-Stacking: B:H.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamura, R. et al., X-ray crystallographic snapshots of the thioazolidine formation upon the PLP during inhibition of SufS by D-cysteine. to be published

Release Date

2023-04-05

Peptides

Cysteine desulfurase IscS: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cysteine desulfurase IscS

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