SMTL ID : 6ksi.1

Staphylococcus aureus lipase - native

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: S.75, D.78, H.98, H.104, D.250 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.78, A:H.98, A:H.104, A:D.250 ZN.10: 4 residues within 4Å: Chain B: D.78, H.98, H.104, D.250 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.78, B:D.78, B:H.98, B:H.104, B:D.250

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: G.297, F.299, D.362, D.365, D.370, D.373 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:G.297, A:D.362, A:D.365, A:D.370, A:D.373 CA.11: 6 residues within 4Å: Chain B: G.297, F.299, D.362, D.365, D.370, D.373 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:G.297, B:D.362, B:D.365, B:D.370, B:D.373

2 x 6NA: HEXANOIC ACID(Non-covalent)

6NA.3: 6 residues within 4Å: Chain A: F.31, A.188, F.192, V.323, V.324 Ligands: BUA.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.188, A:F.192 Hydrogen bonds: A:V.323 Salt bridges: A:H.363 6NA.12: 4 residues within 4Å: Chain B: Y.43, Y.46 Ligands: OCA.15, BUA.16 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.46

3 x DAO: LAURIC ACID(Non-covalent)

DAO.4: 4 residues within 4Å: Chain A: A.204, R.207, F.208, Y.233 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.207 DAO.5: 6 residues within 4Å: Chain A: N.211, K.212, Q.227, S.232, Y.233, I.234 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.234 DAO.13: 3 residues within 4Å: Chain B: A.204, R.207, Y.233 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.204 Hydrogen bonds: B:Y.233 Salt bridges: B:R.207

2 x LEA: PENTANOIC ACID(Non-covalent)

LEA.6: 6 residues within 4Å: Chain A: L.32, Y.43, Y.46, H.129, V.364 Ligands: BUA.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.46 Salt bridges: A:H.129 LEA.14: 4 residues within 4Å: Chain B: F.31, A.189, F.192 Ligands: BUA.16 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.31, B:F.31, B:F.192

2 x OCA: OCTANOIC ACID (CAPRYLIC ACID)(Non-covalent)

OCA.7: 7 residues within 4Å: Chain A: L.32, L.34, P.40, Y.43, F.73, L.205, M.209 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.40, A:L.205 Hydrogen bonds: A:Y.43 OCA.15: 7 residues within 4Å: Chain B: L.32, L.34, P.40, Y.43, F.73, L.205 Ligands: 6NA.12 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.40, B:L.205 Hydrogen bonds: B:Y.43

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.8: 3 residues within 4Å: Chain A: F.192, L.301, T.304 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.192

2 x BUA: butanoic acid(Non-covalent)

BUA.9: 3 residues within 4Å: Chain A: H.363 Ligands: 6NA.3, LEA.6 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.363 BUA.16: 4 residues within 4Å: Chain B: M.302, H.363 Ligands: 6NA.12, LEA.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kitadokoro, K. et al., Crystal structure of pathogenic Staphylococcus aureus lipase complex with the anti-obesity drug orlistat. Sci Rep (2020)

Release Date

2020-04-08

Peptides

Lipase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lipase 2

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