SMTL ID : 7mct.1

Crystal structure of Staphylococcus aureus Cystathionine gamma lyase, Holoenzyme with bound NL1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

20 x LB6: N-[(6-bromo-1H-indol-1-yl)acetyl]glycine(Non-covalent)

LB6.1: 9 residues within 4Å: Chain A: G.100, Y.103, R.104, T.338, H.339, I.342, I.346, E.350, I.352 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.342, A:I.342, A:I.346 Hydrogen bonds: A:G.100 Water bridges: A:V.98, A:R.104, A:R.104, A:N.146, A:H.339 Salt bridges: A:R.104, A:H.339 pi-Stacking: A:Y.103 LB6.2: 6 residues within 4Å: Chain A: S.1, N.2, K.3, T.5, K.6 Ligands: PLP.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.6 Hydrogen bonds: A:K.6 Water bridges: A:K.3, A:N.65 Salt bridges: A:K.6 pi-Cation interactions: A:K.6 LB6.3: 1 residues within 4Å: Chain A: S.54 No protein-ligand interaction detected (PLIP) LB6.4: 4 residues within 4Å: Chain A: L.7, L.63, P.177, Y.178 No protein-ligand interaction detected (PLIP) LB6.5: 2 residues within 4Å: Chain A: H.68, F.70 No protein-ligand interaction detected (PLIP) LB6.14: 9 residues within 4Å: Chain B: G.100, Y.103, R.104, T.338, H.339, I.342, I.346, E.350, I.352 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.342, B:I.342, B:I.346 Hydrogen bonds: B:G.100 Water bridges: B:V.98, B:R.104, B:R.104, B:N.146, B:H.339 Salt bridges: B:R.104, B:H.339 pi-Stacking: B:Y.103 LB6.15: 6 residues within 4Å: Chain B: S.1, N.2, K.3, T.5, K.6 Ligands: PLP.19 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:K.6 Hydrogen bonds: B:K.6 Water bridges: B:K.3, B:N.65 Salt bridges: B:K.6 pi-Cation interactions: B:K.6 LB6.16: 1 residues within 4Å: Chain B: S.54 No protein-ligand interaction detected (PLIP) LB6.17: 4 residues within 4Å: Chain B: L.7, L.63, P.177, Y.178 No protein-ligand interaction detected (PLIP) LB6.18: 2 residues within 4Å: Chain B: H.68, F.70 No protein-ligand interaction detected (PLIP) LB6.27: 9 residues within 4Å: Chain C: G.100, Y.103, R.104, T.338, H.339, I.342, I.346, E.350, I.352 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:I.342, C:I.342, C:I.346 Hydrogen bonds: C:G.100 Water bridges: C:V.98, C:R.104, C:R.104, C:N.146, C:H.339 Salt bridges: C:R.104, C:H.339 pi-Stacking: C:Y.103 LB6.28: 6 residues within 4Å: Chain C: S.1, N.2, K.3, T.5, K.6 Ligands: PLP.32 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:K.6 Hydrogen bonds: C:K.6 Water bridges: C:K.3, C:N.65 Salt bridges: C:K.6 pi-Cation interactions: C:K.6 LB6.29: 1 residues within 4Å: Chain C: S.54 No protein-ligand interaction detected (PLIP) LB6.30: 4 residues within 4Å: Chain C: L.7, L.63, P.177, Y.178 No protein-ligand interaction detected (PLIP) LB6.31: 2 residues within 4Å: Chain C: H.68, F.70 No protein-ligand interaction detected (PLIP) LB6.40: 9 residues within 4Å: Chain D: G.100, Y.103, R.104, T.338, H.339, I.342, I.346, E.350, I.352 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:I.342, D:I.342, D:I.346 Hydrogen bonds: D:G.100 Water bridges: D:V.98, D:R.104, D:R.104, D:N.146, D:H.339 Salt bridges: D:R.104, D:H.339 pi-Stacking: D:Y.103 LB6.41: 6 residues within 4Å: Chain D: S.1, N.2, K.3, T.5, K.6 Ligands: PLP.45 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:K.6 Hydrogen bonds: D:K.6 Water bridges: D:K.3, D:N.65 Salt bridges: D:K.6 pi-Cation interactions: D:K.6 LB6.42: 1 residues within 4Å: Chain D: S.54 No protein-ligand interaction detected (PLIP) LB6.43: 4 residues within 4Å: Chain D: L.7, L.63, P.177, Y.178 No protein-ligand interaction detected (PLIP) LB6.44: 2 residues within 4Å: Chain D: H.68, F.70 No protein-ligand interaction detected (PLIP)

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

PLP.6: 8 residues within 4Å: Chain A: S.1, T.5, K.6, H.9, G.10, N.65 Chain D: Y.317 Ligands: LB6.2 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:H.9 Water bridges: A:K.6, A:N.65 Salt bridges: A:K.6 Hydrogen bonds: D:Y.317 PLP.19: 8 residues within 4Å: Chain B: S.1, T.5, K.6, H.9, G.10, N.65 Chain C: Y.317 Ligands: LB6.15 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:H.9 Water bridges: B:K.6, B:N.65 Salt bridges: B:K.6 PLP.32: 8 residues within 4Å: Chain B: Y.317 Chain C: S.1, T.5, K.6, H.9, G.10, N.65 Ligands: LB6.28 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:H.9 Water bridges: C:K.6, C:N.65 Salt bridges: C:K.6 Hydrogen bonds: B:Y.317 PLP.45: 8 residues within 4Å: Chain A: Y.317 Chain D: S.1, T.5, K.6, H.9, G.10, N.65 Ligands: LB6.41 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:H.9 Water bridges: D:K.6, D:N.65 Salt bridges: D:K.6

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

NA.7: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain A Water bridges: A:I.187, A:S.212 NA.8: 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.20: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain B Water bridges: B:I.187, B:S.212 NA.21: 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.33: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain C Water bridges: C:I.187, C:S.212 NA.34: 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.46: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain D Water bridges: D:I.187, D:S.212 NA.47: 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

20 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: Q.41, G.42, Y.43, A.49, S.54 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain A: L.166, I.167, D.188, D.213, L.216, R.219 Ligand excluded by PLIP GOL.11: 3 residues within 4Å: Chain A: L.85, R.219 Chain C: R.112 Ligand excluded by PLIP GOL.12: 2 residues within 4Å: Chain A: A.340, R.347 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain A: T.123, H.124, T.125, K.156 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain B: Q.41, G.42, Y.43, A.49, S.54 Ligand excluded by PLIP GOL.23: 6 residues within 4Å: Chain B: L.166, I.167, D.188, D.213, L.216, R.219 Ligand excluded by PLIP GOL.24: 3 residues within 4Å: Chain B: L.85, R.219 Chain D: R.112 Ligand excluded by PLIP GOL.25: 2 residues within 4Å: Chain B: A.340, R.347 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain B: T.123, H.124, T.125, K.156 Ligand excluded by PLIP GOL.35: 5 residues within 4Å: Chain C: Q.41, G.42, Y.43, A.49, S.54 Ligand excluded by PLIP GOL.36: 6 residues within 4Å: Chain C: L.166, I.167, D.188, D.213, L.216, R.219 Ligand excluded by PLIP GOL.37: 3 residues within 4Å: Chain A: R.112 Chain C: L.85, R.219 Ligand excluded by PLIP GOL.38: 2 residues within 4Å: Chain C: A.340, R.347 Ligand excluded by PLIP GOL.39: 4 residues within 4Å: Chain C: T.123, H.124, T.125, K.156 Ligand excluded by PLIP GOL.48: 5 residues within 4Å: Chain D: Q.41, G.42, Y.43, A.49, S.54 Ligand excluded by PLIP GOL.49: 6 residues within 4Å: Chain D: L.166, I.167, D.188, D.213, L.216, R.219 Ligand excluded by PLIP GOL.50: 3 residues within 4Å: Chain B: R.112 Chain D: L.85, R.219 Ligand excluded by PLIP GOL.51: 2 residues within 4Å: Chain D: A.340, R.347 Ligand excluded by PLIP GOL.52: 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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