SMTL ID : 7mcq.1

Crystal structure of Staphylococcus aureus Cystathionine gamma lyase, AOAA-bound enzyme in dimeric form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.84 Å

Oligo State

homo-tetramer

Ligands

4 x IK2: 4'-DEOXY-4'-ACETYLYAMINO-PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

IK2.1: 17 residues within 4Å: Chain A: S.74, G.75, V.76, I.79, Y.99, E.142, D.171, T.173, F.174, S.193, T.195, K.196, A.206, E.322, S.323 Chain B: Y.45, R.47 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.99, A:Y.99 Hydrogen bonds: A:G.75, A:V.76, A:Y.99, A:T.195, A:K.196, A:A.206, A:E.322, A:S.323, B:Y.45 Water bridges: A:E.142, A:N.146 Salt bridges: A:K.196, A:K.196, B:R.47 IK2.6: 19 residues within 4Å: Chain A: Y.45, R.47 Chain B: S.74, G.75, V.76, I.79, Y.99, E.142, N.146, D.171, T.173, S.193, T.195, K.196, A.206, S.323, L.324, T.338, R.358 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.99 Hydrogen bonds: B:G.75, B:V.76, B:N.146, B:T.195, B:K.196, B:K.196, B:A.206, B:S.323, B:S.323, A:Y.45 Salt bridges: B:K.196, B:K.196, B:R.358, A:R.47 IK2.11: 17 residues within 4Å: Chain C: S.74, G.75, V.76, I.79, Y.99, E.142, D.171, T.173, F.174, S.193, T.195, K.196, A.206, E.322, S.323 Chain D: Y.45, R.47 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.99, C:Y.99 Hydrogen bonds: C:G.75, C:V.76, C:Y.99, C:K.196, C:A.206, C:S.323 Water bridges: C:E.142, C:N.146 Salt bridges: C:K.196, C:K.196, D:R.47 IK2.16: 19 residues within 4Å: Chain C: Y.45, R.47 Chain D: S.74, G.75, V.76, I.79, Y.99, E.142, N.146, D.171, T.173, S.193, T.195, K.196, A.206, S.323, L.324, T.338, R.358 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.99 Hydrogen bonds: D:G.75, D:V.76, D:N.146, D:T.173, D:K.196, D:K.196, D:A.206, D:S.323, D:S.323 Salt bridges: D:K.196, D:K.196, D:R.358, C:R.47

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

NA.2: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.162 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.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.8: 2 residues within 4Å: Chain B: H.9, G.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.11 NA.12: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.162, C:K.162 NA.13: 2 residues within 4Å: Chain C: H.9, G.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.9 NA.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.18: 2 residues within 4Å: Chain D: H.9, G.11 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.11

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: Q.41, G.42, Y.43, A.49, S.54 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.57 GOL.5: 3 residues within 4Å: Chain A: H.124, T.125, K.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.125, A:K.156 GOL.9: 3 residues within 4Å: Chain A: R.112 Chain B: L.85, R.219 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.219 GOL.10: 3 residues within 4Å: Chain B: H.124, T.125, K.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.125, B:T.125 GOL.14: 5 residues within 4Å: Chain C: Q.41, G.42, Y.43, A.49, S.54 1 PLIP interactions: 1 interactions with chain C Water bridges: C:E.57 GOL.15: 3 residues within 4Å: Chain C: H.124, T.125, K.156 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.125, C:K.156 GOL.19: 3 residues within 4Å: Chain C: R.112 Chain D: L.85, R.219 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.219 GOL.20: 3 residues within 4Å: Chain D: H.124, T.125, K.156 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.125, D:T.125

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
A

B
H

C
A

D
H

Bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase

Related Entries With Identical Sequence