SMTL ID : 6ksm.1

Staphylococcus aureus lipase -Orlistat complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: 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.7: 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.8: 5 residues within 4Å: Chain B: G.297, 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 DH9: (2S,3S,5S)-5-[(N-FORMYL-L-LEUCYL)OXY]-2-HEXYL-3-HYDROXYHEXADECANOIC ACID(Covalent)

DH9.3: 17 residues within 4Å: Chain A: G.30, F.31, L.32, Y.43, Y.46, H.129, S.130, M.131, A.188, L.256, L.301, T.304, V.323, V.324, H.363, V.364, I.367 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.31, A:L.32, A:Y.46, A:A.188, A:L.256, A:L.301, A:V.324, A:I.367 Hydrogen bonds: A:F.31, A:M.131, A:H.363 Salt bridges: A:H.363, A:H.363 DH9.9: 22 residues within 4Å: Chain B: G.30, F.31, L.32, Y.43, Y.46, H.129, S.130, M.131, A.188, A.189, F.192, L.256, F.299, L.301, V.323, V.324, H.363, V.364, I.367, V.369, F.371 Ligands: STE.12 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.31, B:F.31, B:L.32, B:A.188, B:L.256, B:F.299, B:L.301, B:L.301, B:V.323, B:V.323, B:V.324, B:I.367, B:F.371 Hydrogen bonds: B:F.31, B:M.131, B:H.363 Salt bridges: B:H.363, B:H.363

4 x DAO: LAURIC ACID(Non-covalent)

DAO.4: 3 residues within 4Å: Chain A: A.204, R.207, Y.233 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.204 Hydrogen bonds: A:A.204 Salt bridges: A:R.207 DAO.5: 4 residues within 4Å: Chain A: A.41, L.42, Y.43 Ligands: DAO.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.41, A:L.42 DAO.10: 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 DAO.11: 4 residues within 4Å: Chain B: L.301, T.304 Ligands: DAO.5, BUA.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.301

2 x BUA: butanoic acid(Non-functional Binders)

BUA.6: 1 residues within 4Å: Ligands: DAO.11 No protein-ligand interaction detected (PLIP) BUA.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x STE: STEARIC ACID(Non-covalent)

STE.12: 3 residues within 4Å: Chain B: L.42, M.209 Ligands: DH9.9 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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