SMTL ID : 5wt4.1

L-Cysteine-PLP intermediate of NifS from Helicobacter pylori

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.92 Å

Oligo State

homo-dimer

Ligands

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

IPA.1: 4 residues within 4Å: Chain A: Y.56, D.66, V.67, N.235 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.67 IPA.3: 4 residues within 4Å: Chain B: Y.56, D.66, V.67, N.235 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.56, B:V.67

2 x C6P: N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-CYSTEINE(Non-covalent)

C6P.2: 17 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, R.354 Chain B: N.33, G.240, T.241 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.182, A:Q.183 Hydrogen bonds: A:A.73, 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 C6P.4: 17 residues within 4Å: Chain A: N.33, 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, R.354 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.182, B:Q.183 Hydrogen bonds: B:A.73, B:T.74, B:N.155, B:Q.183, B:S.203, B:K.206, A:T.241, A:T.241 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., Snapshots of PLP-substrate and PLP-product external aldimines as intermediates in two types of cysteine desulfurase enzymes. Febs J. (2019)

Release Date

2017-12-13

Peptides

Cysteine desulfurase IscS: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cysteine desulfurase IscS

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