SMTL ID : 7xet.1

SufS with beta-cyano-L-alanine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x 9YC: (2~{E})-3-cyano-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylimino]propanoic acid(Non-covalent)

9YC.1: 18 residues within 4Å: Chain A: A.31, A.32, T.95, T.96, H.124, A.126, N.176, D.201, A.203, S.224, H.226, K.227, R.359, R.379 Chain B: N.54, R.57, G.277, T.278 22 PLIP interactions: 16 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:A.203 Hydrogen bonds: A:T.95, A:T.96, A:T.96, A:N.176, A:S.224, A:K.227, B:R.57, B:T.278, B:T.278 Water bridges: A:K.93, A:G.94, A:T.97, A:S.224, B:E.255, B:T.278, B:T.278 Salt bridges: A:H.226, A:K.227, A:R.359, A:R.379 pi-Stacking: A:H.124 9YC.7: 18 residues within 4Å: Chain A: N.54, R.57, G.277, T.278 Chain B: A.31, A.32, T.95, T.96, H.124, A.126, N.176, D.201, A.203, S.224, H.226, K.227, R.359, R.379 20 PLIP interactions: 4 interactions with chain A, 16 interactions with chain B Hydrogen bonds: A:R.57, A:T.278, B:T.95, B:T.96, B:T.96, B:N.176, B:S.224, B:K.227 Water bridges: A:T.278, A:T.278, B:K.93, B:G.94, B:T.97, B:S.224 Hydrophobic interactions: B:A.203 Salt bridges: B:H.226, B:K.227, B:R.359, B:R.379 pi-Stacking: B:H.124

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

PEG.2: 4 residues within 4Å: Chain A: H.56, E.255, K.268, W.272 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.255, A:E.255, A:K.268 PEG.3: 5 residues within 4Å: Chain A: T.7, R.10, T.387, E.389, E.390 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.7, A:T.387, A:E.389 Water bridges: A:R.10, A:T.387, A:E.389 PEG.5: 4 residues within 4Å: Chain A: R.78, N.82, A.83, Q.214 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.78, A:R.78, A:Q.214, A:Q.214 Water bridges: A:N.82 PEG.6: 4 residues within 4Å: Chain A: V.181, M.209, S.303, R.331 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.303 Water bridges: A:K.210, A:D.300, A:S.303 PEG.8: 4 residues within 4Å: Chain B: H.56, E.255, K.268, W.272 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.56, B:E.255, B:K.268 Water bridges: B:E.269 PEG.9: 5 residues within 4Å: Chain B: T.7, R.10, T.387, E.389, E.390 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.7 Water bridges: B:R.10, B:T.387, B:E.389 PEG.11: 4 residues within 4Å: Chain B: R.78, N.82, A.83, Q.214 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.78, B:R.78, B:Q.214, B:Q.214 Water bridges: B:N.82 PEG.12: 4 residues within 4Å: Chain B: V.181, M.209, S.303, R.331 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.303 Water bridges: B:K.210, B:D.300, B:D.300

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 6 residues within 4Å: Chain A: D.45, K.46, N.49, Q.50 Chain B: P.14, Q.18 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.45, A:N.49, A:Q.50, B:Q.18 PGE.10: 6 residues within 4Å: Chain A: P.14, Q.18 Chain B: D.45, K.46, N.49, Q.50 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.18, B:D.45, B:N.49, B:Q.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamura, R. et al., Inhibition mechanism of SufS by L-propargylglycine. to be published

Release Date

2023-04-05

Peptides

Cysteine desulfurase SufS: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cysteine desulfurase SufS

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