SMTL ID : 7xep.1

SufS with L-propargylglycine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

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

PEG.1: 5 residues within 4Å: Chain A: T.7, R.10, T.387, E.389, E.390 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.387, A:E.389, A:E.389 Water bridges: A:I.6, A:R.10 PEG.2: 4 residues within 4Å: Chain A: N.49, Q.50 Chain B: P.14, Q.18 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.18, A:Q.50 PEG.3: 5 residues within 4Å: Chain A: V.350, E.354, A.397, K.400, Y.404 No protein-ligand interaction detected (PLIP) PEG.5: 5 residues within 4Å: Chain A: R.10, L.16, H.17, Q.18, D.24 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.10, A:Q.18 Water bridges: A:R.10, A:H.17 PEG.6: 5 residues within 4Å: Chain A: V.181, M.209, S.303, H.307, R.331 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.303 Water bridges: A:K.210, A:D.300, A:S.303, A:E.330 PEG.7: 7 residues within 4Å: Chain A: N.338, L.339, V.342, P.344, V.374, T.375, A.376 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.339, A:T.375 Water bridges: A:L.339 PEG.9: 4 residues within 4Å: Chain A: R.57, 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.13: 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, B:E.389 Water bridges: B:I.6, B:R.10 PEG.14: 4 residues within 4Å: Chain A: P.14, Q.18 Chain B: N.49, Q.50 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.18, B:Q.50 PEG.15: 5 residues within 4Å: Chain B: V.350, E.354, A.397, K.400, Y.404 No protein-ligand interaction detected (PLIP) PEG.17: 5 residues within 4Å: Chain B: R.10, L.16, H.17, Q.18, D.24 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.10, B:Q.18 Water bridges: B:R.10, B:H.17 PEG.18: 5 residues within 4Å: Chain B: V.181, M.209, S.303, H.307, R.331 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.303 Water bridges: B:K.210, B:D.300, B:D.300, B:E.330 PEG.19: 7 residues within 4Å: Chain B: N.338, L.339, V.342, P.344, V.374, T.375, A.376 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.339, B:T.375 Water bridges: B:L.339 PEG.21: 4 residues within 4Å: Chain B: R.57, E.255, K.268, W.272 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.255, B:K.268

2 x EIL: [6-methyl-4-[[(5-methyl-2-oxidanylidene-furan-3-ylidene)amino]methyl]-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate(Non-covalent)

EIL.4: 17 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.359, R.379 Chain B: N.54, G.277, T.278 20 PLIP interactions: 15 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:A.32, A:A.203, B:N.54 Hydrogen bonds: 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:R.379, B:T.278, B:T.278 Salt bridges: A:H.226, A:K.227, A:R.379 pi-Stacking: A:H.124 EIL.16: 17 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.359, R.379 19 PLIP interactions: 15 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.32, B:A.203, A:N.54 Hydrogen bonds: 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:R.379, A:T.278, A:T.278 Salt bridges: B:H.226, B:K.227, B:R.379 pi-Stacking: B:H.124

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

EDO.8: 4 residues within 4Å: Chain A: M.86, L.270, P.271, W.272 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.270 EDO.10: 4 residues within 4Å: Chain A: D.8, I.9, Q.12 Ligands: EDO.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.8, A:Q.12 Water bridges: A:D.8 EDO.11: 5 residues within 4Å: Chain A: Q.12, F.293, E.296, I.297 Ligands: EDO.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.12, A:Q.12, A:I.297 EDO.12: 2 residues within 4Å: Chain A: A.39, T.43 No protein-ligand interaction detected (PLIP) EDO.20: 4 residues within 4Å: Chain B: M.86, L.270, P.271, W.272 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.270 EDO.22: 4 residues within 4Å: Chain B: D.8, I.9, Q.12 Ligands: EDO.23 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.8, B:Q.12 EDO.23: 5 residues within 4Å: Chain B: Q.12, F.293, E.296, I.297 Ligands: EDO.22 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.12, B:Q.12, B:I.297 Water bridges: B:E.296 EDO.24: 2 residues within 4Å: Chain B: A.39, T.43 No protein-ligand interaction detected (PLIP)

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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