SMTL ID : 7xes.1

NifS with L-penicillamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

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

IPA.1: 5 residues within 4Å: Chain A: Y.56, D.66, V.67, I.68, N.235 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.66, A:V.67 IPA.4: 5 residues within 4Å: Chain B: Y.56, D.66, V.67, I.68, N.235 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.56, B:D.66, B:D.66, B:V.67

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 9ZN: (2~{R})-3-methyl-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-sulfanyl-butanoic acid(Non-covalent)

9ZN.3: 16 residues within 4Å: Chain A: N.10, C.72, A.73, T.74, H.104, N.155, D.180, V.182, Q.183, S.203, H.205, K.206, R.354 Chain B: E.232, G.240, T.241 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.182, A:Q.183 Hydrogen bonds: A:T.74, A:T.74, A:N.155, A:Q.183, A:S.203, A:K.206, B:T.241 Salt bridges: A:H.205, A:K.206, A:R.354 pi-Stacking: A:H.104 9ZN.6: 16 residues within 4Å: Chain A: E.232, G.240, T.241 Chain B: N.10, C.72, A.73, T.74, H.104, N.155, D.180, V.182, Q.183, S.203, H.205, K.206, R.354 13 PLIP interactions: 2 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:T.241, A:T.241, B:T.74, B:N.155, B:Q.183, B:S.203, B:K.206 Hydrophobic interactions: B:V.182, B:Q.183 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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