SMTL ID : 7mcb.1

Crystal structure of Staphylococcus aureus Cystathionine gamma lyase Holoenzyme

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 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 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:H.9 Salt bridges: A:K.6 Hydrogen bonds: D:Y.317 PLP.8: 7 residues within 4Å: Chain B: S.1, T.5, K.6, H.9, G.10, N.65 Chain C: Y.317 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:H.9 Salt bridges: B:K.6 PLP.15: 7 residues within 4Å: Chain B: Y.317 Chain C: S.1, T.5, K.6, H.9, G.10, N.65 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:H.9 Salt bridges: C:K.6 Hydrogen bonds: B:Y.317 PLP.22: 7 residues within 4Å: Chain A: Y.317 Chain D: S.1, T.5, K.6, H.9, G.10, N.65 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:H.9 Salt bridges: D:K.6

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

NA.2: 0 residues within 4Å: (No contacts) 4 PLIP interactions: 4 interactions with chain A Water bridges: A:G.186, A:I.187, A:D.188, A:D.188 NA.3: 2 residues within 4Å: Chain A: H.9, G.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.9 NA.9: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain B Water bridges: B:L.183, B:D.188 NA.10: 2 residues within 4Å: Chain B: H.9, G.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.11 Water bridges: B:T.13 NA.16: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain C Water bridges: C:D.188, C:D.188 NA.17: 2 residues within 4Å: Chain C: H.9, G.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.11 NA.23: 0 residues within 4Å: (No contacts) 4 PLIP interactions: 4 interactions with chain D Water bridges: D:L.183, D:G.186, D:I.187, D:D.188 NA.24: 2 residues within 4Å: Chain D: H.9, G.11 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.9 Water bridges: D:T.13

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: T.123, H.124, T.125, K.156, N.283 Ligand excluded by PLIP GOL.5: 4 residues within 4Å: Chain A: Q.41, G.42, Y.43, S.54 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: G.165, L.166, I.167, D.188, L.216, R.219 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain A: Q.265, S.277, I.278, E.279 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain B: T.123, H.124, T.125, K.156, N.283 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain B: Q.41, G.42, Y.43, S.54 Ligand excluded by PLIP GOL.13: 6 residues within 4Å: Chain B: G.165, L.166, I.167, D.188, L.216, R.219 Ligand excluded by PLIP GOL.14: 4 residues within 4Å: Chain B: Q.265, S.277, I.278, E.279 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain C: T.123, H.124, T.125, K.156, N.283 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain C: Q.41, G.42, Y.43, S.54 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain C: G.165, L.166, I.167, D.188, L.216, R.219 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain C: Q.265, S.277, I.278, E.279 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain D: T.123, H.124, T.125, K.156, N.283 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain D: Q.41, G.42, Y.43, S.54 Ligand excluded by PLIP GOL.27: 6 residues within 4Å: Chain D: G.165, L.166, I.167, D.188, L.216, R.219 Ligand excluded by PLIP GOL.28: 4 residues within 4Å: Chain D: Q.265, S.277, I.278, E.279 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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