SMTL ID : 7xek.1

SufS with D-cysteine for 6 h

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

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.1: 16 residues within 4Å: Chain A: A.31, A.32, T.95, T.96, H.124, V.174, N.176, D.201, A.203, S.224, H.226, K.227, R.379 Chain B: N.54, G.277, T.278 23 PLIP interactions: 18 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:N.176, A:A.203 Hydrogen bonds: A:T.95, A:T.96, A:T.96, A:N.176, A:S.224, A:K.227, B:T.278, B:T.278 Water bridges: A:K.93, A:K.93, A:T.97, A:S.224, A:R.379, A:R.379, B:N.54, B:T.278, B:T.278 Salt bridges: A:H.226, A:K.227, A:R.379 pi-Stacking: A:H.124 9YX.16: 16 residues within 4Å: Chain A: N.54, G.277, T.278 Chain B: A.31, A.32, T.95, T.96, H.124, V.174, N.176, D.201, A.203, S.224, H.226, K.227, R.379 22 PLIP interactions: 18 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:N.176, B:A.203 Hydrogen bonds: B:T.95, B:T.96, B:T.96, B:N.176, B:S.224, B:K.227, A:T.278 Water bridges: B:K.93, B:K.93, B:T.97, B:S.224, B:H.363, B:R.379, A:N.54, A:T.278, A:T.278 Salt bridges: B:H.226, B:K.227, B:R.379 pi-Stacking: B:H.124

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

PEG.2: 3 residues within 4Å: Chain A: K.46, Y.51, R.65 Ligand excluded by PLIP PEG.3: 4 residues within 4Å: Chain A: A.39, E.42, T.43, K.46 Ligand excluded by PLIP PEG.4: 7 residues within 4Å: Chain A: H.307, A.310, A.311, L.314, E.329, E.330, R.331 Ligand excluded by PLIP PEG.7: 6 residues within 4Å: Chain A: N.49, Q.50 Chain B: P.14, H.17, Q.18 Ligands: PEG.25 Ligand excluded by PLIP PEG.8: 3 residues within 4Å: Chain A: D.8, F.293, E.296 Ligand excluded by PLIP PEG.9: 3 residues within 4Å: Chain A: H.192, A.196, L.243 Ligand excluded by PLIP PEG.10: 5 residues within 4Å: Chain A: E.11, P.14, H.17, R.38 Ligands: PEG.22 Ligand excluded by PLIP PEG.11: 3 residues within 4Å: Chain A: M.4, H.305, K.308 Ligand excluded by PLIP PEG.12: 6 residues within 4Å: Chain A: R.10, L.16, H.17, Q.18, D.24 Ligands: PGE.15 Ligand excluded by PLIP PEG.13: 5 residues within 4Å: Chain A: V.59, H.60, T.61, T.64 Chain B: D.352 Ligand excluded by PLIP PEG.17: 3 residues within 4Å: Chain B: K.46, Y.51, R.65 Ligand excluded by PLIP PEG.18: 4 residues within 4Å: Chain B: A.39, E.42, T.43, K.46 Ligand excluded by PLIP PEG.19: 7 residues within 4Å: Chain B: H.307, A.310, A.311, L.314, E.329, E.330, R.331 Ligand excluded by PLIP PEG.22: 6 residues within 4Å: Chain A: P.14, H.17, Q.18 Chain B: N.49, Q.50 Ligands: PEG.10 Ligand excluded by PLIP PEG.23: 3 residues within 4Å: Chain B: D.8, F.293, E.296 Ligand excluded by PLIP PEG.24: 3 residues within 4Å: Chain B: H.192, A.196, L.243 Ligand excluded by PLIP PEG.25: 5 residues within 4Å: Chain B: E.11, P.14, H.17, R.38 Ligands: PEG.7 Ligand excluded by PLIP PEG.26: 3 residues within 4Å: Chain B: M.4, H.305, K.308 Ligand excluded by PLIP PEG.27: 6 residues within 4Å: Chain B: R.10, L.16, H.17, Q.18, D.24 Ligands: PGE.30 Ligand excluded by PLIP PEG.28: 5 residues within 4Å: Chain A: D.352 Chain B: V.59, H.60, T.61, T.64 Ligand excluded by PLIP

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 2 residues within 4Å: Chain A: V.181, S.303 No protein-ligand interaction detected (PLIP) EDO.14: 5 residues within 4Å: Chain A: E.149, Y.326, G.327, W.371, L.372 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.327 EDO.20: 2 residues within 4Å: Chain B: V.181, S.303 No protein-ligand interaction detected (PLIP) EDO.29: 5 residues within 4Å: Chain B: E.149, Y.326, G.327, W.371, L.372 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.327

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 6 residues within 4Å: Chain A: H.56, R.57, E.255, K.268, W.272 Chain B: H.362 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.268 PG4.21: 6 residues within 4Å: Chain A: H.362 Chain B: H.56, R.57, E.255, K.268, W.272 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.268, B:E.269

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

PGE.15: 7 residues within 4Å: Chain A: I.6, T.7, R.10, T.387, E.389, E.390 Ligands: PEG.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.387, A:T.387 Water bridges: A:R.10 PGE.30: 7 residues within 4Å: Chain B: I.6, T.7, R.10, T.387, E.389, E.390 Ligands: PEG.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.387 Water bridges: B:R.10

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 SufS: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cysteine desulfurase SufS

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