SMTL ID : 7mcu.1

Crystal structure of Staphylococcus aureus Cystathionine gamma lyase, Holoenzyme with bound NL2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 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.9: 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.17: 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.25: 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

4 x YXA: 5-[(6-bromo-1H-indol-1-yl)methyl]-2-methylfuran-3-carboxylic acid(Non-covalent)

YXA.2: 9 residues within 4Å: Chain A: G.100, Y.103, R.104, T.338, H.339, I.342, I.346, E.350, I.352 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.103, A:I.342, A:I.342, A:I.346, A:E.350 Salt bridges: A:R.104 pi-Stacking: A:Y.103 YXA.10: 9 residues within 4Å: Chain B: G.100, Y.103, R.104, T.338, H.339, I.342, I.346, E.350, I.352 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.103, B:I.342, B:I.342, B:I.346, B:E.350 Salt bridges: B:R.104 pi-Stacking: B:Y.103 YXA.18: 9 residues within 4Å: Chain C: G.100, Y.103, R.104, T.338, H.339, I.342, I.346, E.350, I.352 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.103, C:I.342, C:I.342, C:I.346, C:E.350 Salt bridges: C:R.104 pi-Stacking: C:Y.103 YXA.26: 9 residues within 4Å: Chain D: G.100, Y.103, R.104, T.338, H.339, I.342, I.346, E.350, I.352 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.103, D:I.342, D:I.342, D:I.346, D:E.350 Salt bridges: D:R.104 pi-Stacking: D:Y.103

4 x FLC: CITRATE ANION(Non-covalent)

FLC.3: 5 residues within 4Å: Chain A: A.340, I.342, P.343, A.344, R.347 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.342, A:A.344 Salt bridges: A:R.347, A:R.347 FLC.11: 5 residues within 4Å: Chain B: A.340, I.342, P.343, A.344, R.347 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.342, B:A.344 Salt bridges: B:R.347, B:R.347 FLC.19: 5 residues within 4Å: Chain C: A.340, I.342, P.343, A.344, R.347 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:I.342, C:A.344 Salt bridges: C:R.347, C:R.347 FLC.27: 5 residues within 4Å: Chain D: A.340, I.342, P.343, A.344, R.347 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:I.342, D:A.344 Salt bridges: D:R.347, D:R.347

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

NA.4: 0 residues within 4Å: (No contacts) 5 PLIP interactions: 5 interactions with chain A Water bridges: A:G.186, A:I.187, A:D.188, A:D.188, A:D.188 NA.5: 2 residues within 4Å: Chain A: H.9, G.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.10 NA.12: 0 residues within 4Å: (No contacts) 7 PLIP interactions: 7 interactions with chain B Water bridges: B:G.186, B:I.187, B:I.187, B:I.187, B:D.188, B:D.188, B:S.212 NA.13: 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.20: 0 residues within 4Å: (No contacts) 6 PLIP interactions: 6 interactions with chain C Water bridges: C:G.186, C:G.186, C:I.187, C:D.188, C:D.188, C:D.188 NA.21: 2 residues within 4Å: Chain C: H.9, G.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.11 NA.28: 0 residues within 4Å: (No contacts) 4 PLIP interactions: 4 interactions with chain D Water bridges: D:G.186, D:I.187, D:D.188, D:S.212 NA.29: 2 residues within 4Å: Chain D: H.9, G.11 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.13 Water bridges: D:T.13

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: T.123, H.124, T.125, K.156, N.283 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.124, A:T.125, A:N.283 Water bridges: A:T.123, A:D.153 GOL.7: 5 residues within 4Å: Chain A: Q.41, G.42, Y.43, A.49, S.54 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.42, A:S.54 Water bridges: A:E.57 GOL.8: 6 residues within 4Å: Chain A: G.165, L.166, I.167, D.188, L.216, R.219 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.165, A:D.188, A:R.219 GOL.14: 5 residues within 4Å: Chain B: T.123, H.124, T.125, K.156, N.283 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.124, B:T.125, B:N.283 Water bridges: B:T.123, B:D.153 GOL.15: 5 residues within 4Å: Chain B: Q.41, G.42, Y.43, A.49, S.54 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.42, B:S.54 Water bridges: B:E.57 GOL.16: 6 residues within 4Å: Chain B: G.165, L.166, I.167, D.188, L.216, R.219 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.165, B:D.188, B:R.219 GOL.22: 5 residues within 4Å: Chain C: T.123, H.124, T.125, K.156, N.283 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.124, C:T.125, C:N.283 Water bridges: C:T.123, C:D.153 GOL.23: 5 residues within 4Å: Chain C: Q.41, G.42, Y.43, A.49, S.54 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.42, C:S.54 Water bridges: C:E.57 GOL.24: 6 residues within 4Å: Chain C: G.165, L.166, I.167, D.188, L.216, R.219 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.165, C:D.188, C:R.219 GOL.30: 5 residues within 4Å: Chain D: T.123, H.124, T.125, K.156, N.283 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:H.124, D:T.125, D:N.283 Water bridges: D:T.123, D:D.153 GOL.31: 5 residues within 4Å: Chain D: Q.41, G.42, Y.43, A.49, S.54 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.42, D:S.54 Water bridges: D:E.57 GOL.32: 6 residues within 4Å: Chain D: G.165, L.166, I.167, D.188, L.216, R.219 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.165, D:D.188, D:R.219

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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