SMTL ID : 7mcy.1

Crystal structure of Staphylococcus aureus Cystathionine gamma lyase, Holoenzyme with bound NL3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-tetramer

Ligands

4 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 7 residues within 4Å: Chain A: S.1, T.5, K.6, H.9, G.10, N.65 Chain D: Y.317 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:H.9 Hydrogen bonds: A:S.1, D:Y.317 Water bridges: A:K.6, A:K.6, A:N.65 Salt bridges: A:K.6 PLP.11: 7 residues within 4Å: Chain B: S.1, T.5, K.6, H.9, G.10, N.65 Chain C: Y.317 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:H.9 Water bridges: B:K.6, B:K.6, B:N.65 Salt bridges: B:K.6 PLP.21: 7 residues within 4Å: Chain B: Y.317 Chain C: S.1, T.5, K.6, H.9, G.10, N.65 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:H.9 Hydrogen bonds: C:S.1, B:Y.317 Water bridges: C:K.6, C:K.6, C:N.65 Salt bridges: C:K.6 PLP.31: 7 residues within 4Å: Chain A: Y.317 Chain D: S.1, T.5, K.6, H.9, G.10, N.65 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:H.9 Water bridges: D:K.6, D:K.6, D:N.65 Salt bridges: D:K.6

4 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 12 residues within 4Å: Chain A: Y.99, R.104, K.196, E.322, S.323, L.324, R.358 Chain C: Y.45, R.47, T.48, N.225 Ligands: NL3.3 11 PLIP interactions: 5 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:T.48, C:N.225, A:S.323, A:R.358 Water bridges: C:T.48, C:T.48, A:R.358 Salt bridges: C:R.47, A:R.104, A:E.322, A:E.322 EPE.12: 12 residues within 4Å: Chain B: Y.99, R.104, K.196, E.322, S.323, L.324, R.358 Chain D: Y.45, R.47, T.48, N.225 Ligands: NL3.13 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:S.323, B:R.358, D:T.48, D:N.225 Water bridges: B:R.358 Salt bridges: B:R.104, B:E.322, B:E.322, D:R.47 EPE.22: 12 residues within 4Å: Chain A: Y.45, R.47, T.48, N.225 Chain C: Y.99, R.104, K.196, E.322, S.323, L.324, R.358 Ligands: NL3.23 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:S.323, C:R.358, A:T.48, A:N.225 Water bridges: C:R.358, A:T.48, A:T.48 Salt bridges: C:R.104, C:E.322, C:E.322, A:R.47 EPE.32: 12 residues within 4Å: Chain B: Y.45, R.47, T.48, N.225 Chain D: Y.99, R.104, K.196, E.322, S.323, L.324, R.358 Ligands: NL3.33 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain D Hydrogen bonds: B:T.48, B:N.225, D:S.323, D:R.358 Salt bridges: B:R.47, D:R.104, D:E.322, D:E.322 Water bridges: D:R.358

4 x NL3: 3-{[6-(7-chloro-1-benzothiophen-2-yl)-1H-indol-1-yl]methyl}-1H-pyrazole-5-carboxylic acid(Non-covalent)

NL3.3: 13 residues within 4Å: Chain A: S.96, D.97, V.98, Y.99, G.100, Y.103, N.146, P.147, T.338, H.339, I.342, I.352 Ligands: EPE.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.99, A:T.338, A:I.342 Hydrogen bonds: A:V.98, A:N.146 Water bridges: A:R.150 Salt bridges: A:H.339 pi-Stacking: A:Y.103 Halogen bonds: A:V.98 NL3.13: 13 residues within 4Å: Chain B: S.96, D.97, V.98, Y.99, G.100, Y.103, N.146, P.147, T.338, H.339, I.342, I.352 Ligands: EPE.12 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.99, B:T.338, B:I.342 Hydrogen bonds: B:V.98, B:N.146 Water bridges: B:R.150 Salt bridges: B:H.339 pi-Stacking: B:Y.103 Halogen bonds: B:V.98 NL3.23: 13 residues within 4Å: Chain C: S.96, D.97, V.98, Y.99, G.100, Y.103, N.146, P.147, T.338, H.339, I.342, I.352 Ligands: EPE.22 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:Y.99, C:T.338, C:I.342 Hydrogen bonds: C:V.98, C:N.146 Water bridges: C:R.150 Salt bridges: C:H.339 pi-Stacking: C:Y.103 Halogen bonds: C:V.98 NL3.33: 13 residues within 4Å: Chain D: S.96, D.97, V.98, Y.99, G.100, Y.103, N.146, P.147, T.338, H.339, I.342, I.352 Ligands: EPE.32 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:Y.99, D:T.338, D:I.342 Hydrogen bonds: D:V.98, D:N.146 Water bridges: D:R.150 Salt bridges: D:H.339 pi-Stacking: D:Y.103 Halogen bonds: D:V.98

12 x NA: SODIUM ION(Non-functional Binders)

NA.4: 0 residues within 4Å: (No contacts) 4 PLIP interactions: 4 interactions with chain A Water bridges: A:I.187, A:I.187, A:I.187, A:S.212 NA.5: 3 residues within 4Å: Chain A: H.9, G.10, G.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.9 NA.6: 4 residues within 4Å: Chain A: L.264, Q.265, H.267, V.270 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.267, A:V.270 NA.14: 0 residues within 4Å: (No contacts) 3 PLIP interactions: 3 interactions with chain B Water bridges: B:I.187, B:I.187, B:S.212 NA.15: 3 residues within 4Å: Chain B: H.9, G.10, G.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.10 Water bridges: B:T.13 NA.16: 4 residues within 4Å: Chain B: L.264, Q.265, H.267, V.270 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.265, B:H.267 NA.24: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain C Water bridges: C:I.187 NA.25: 3 residues within 4Å: Chain C: H.9, G.10, G.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.11 NA.26: 4 residues within 4Å: Chain C: L.264, Q.265, H.267, V.270 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.264, C:H.267 NA.34: 0 residues within 4Å: (No contacts) 3 PLIP interactions: 3 interactions with chain D Water bridges: D:I.187, D:I.187, D:S.212 NA.35: 3 residues within 4Å: Chain D: H.9, G.10, G.11 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.9 Water bridges: D:T.13 NA.36: 4 residues within 4Å: Chain D: L.264, Q.265, H.267, V.270 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.267, D:V.270

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: L.166, I.167, D.188, L.216 Ligand excluded by PLIP GOL.8: 3 residues within 4Å: Chain A: R.112 Chain C: L.85, R.219 Ligand excluded by PLIP GOL.9: 4 residues within 4Å: Chain A: Q.41, G.42, Y.43, S.54 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain A: T.123, H.124, T.125, K.156 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain B: L.166, I.167, D.188, L.216 Ligand excluded by PLIP GOL.18: 3 residues within 4Å: Chain B: R.112 Chain D: L.85, R.219 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain B: Q.41, G.42, Y.43, S.54 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain B: T.123, H.124, T.125, K.156 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain C: L.166, I.167, D.188, L.216 Ligand excluded by PLIP GOL.28: 3 residues within 4Å: Chain A: L.85, R.219 Chain C: R.112 Ligand excluded by PLIP GOL.29: 4 residues within 4Å: Chain C: Q.41, G.42, Y.43, S.54 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain C: T.123, H.124, T.125, K.156 Ligand excluded by PLIP GOL.37: 4 residues within 4Å: Chain D: L.166, I.167, D.188, L.216 Ligand excluded by PLIP GOL.38: 3 residues within 4Å: Chain B: L.85, R.219 Chain D: R.112 Ligand excluded by PLIP GOL.39: 4 residues within 4Å: Chain D: Q.41, G.42, Y.43, S.54 Ligand excluded by PLIP GOL.40: 4 residues within 4Å: Chain D: T.123, H.124, T.125, K.156 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shatalin, K. et al., Inhibitors of bacterial H 2 S biogenesis targeting antibiotic resistance and tolerance. Science (2021)

Release Date

2021-06-23

Peptides

Bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
H

C
H

D
H

Bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase

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