SMTL ID : 7q4j.1

A thermostable lipase from Thermoanaerobacter thermohydrosulfuricus in complex a monoacylglycerol intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

2 x STE: STEARIC ACID(Non-covalent)

STE.1: 18 residues within 4Å: Chain A: G.36, F.37, S.113, M.114, M.142, L.145, I.146, E.149, S.150, Y.154, G.155, M.158, I.166, L.171, V.176, H.233 Ligands: OCT.3, GOL.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.37, A:L.145, A:L.145, A:I.146, A:E.149, A:E.149, A:Y.154, A:I.166, A:L.171, A:V.176 Hydrogen bonds: A:F.37 STE.12: 18 residues within 4Å: Chain B: G.36, F.37, S.113, M.114, M.142, L.145, I.146, E.149, S.150, Y.154, G.155, M.158, I.166, L.171, V.176, A.205 Ligands: GOL.13, D10.18 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.145, B:I.146, B:E.149, B:E.149, B:I.166, B:L.171, B:V.176, B:V.176, B:A.205 Hydrogen bonds: B:F.37

2 x OCT: N-OCTANE(Non-covalent)

OCT.2: 3 residues within 4Å: Chain A: N.202, D.203, E.204 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.204 OCT.3: 6 residues within 4Å: Chain A: F.37, T.38, A.205, H.233 Ligands: STE.1, GOL.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.205

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: G.36, F.37, G.39, E.43, S.113, H.233 Ligands: STE.1, OCT.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.36, A:G.36, A:F.37, A:G.39, A:S.113, A:S.113 Water bridges: A:N.40, A:E.43 GOL.5: 3 residues within 4Å: Chain A: T.201, E.229, N.230 No protein-ligand interaction detected (PLIP) GOL.6: 2 residues within 4Å: Chain A: R.225, T.227 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.225, A:R.225, A:T.227 Water bridges: A:R.225, A:R.225, A:T.227 GOL.13: 9 residues within 4Å: Chain B: G.36, F.37, G.39, E.43, S.113, H.233, T.234 Ligands: STE.12, D10.18 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.36, B:G.36, B:F.37, B:G.39, B:S.113, B:S.113 Water bridges: B:N.40, B:E.43 GOL.14: 8 residues within 4Å: Chain A: K.50, L.238 Chain B: D.76, F.77, S.78, G.168, H.169, K.170 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.76, B:F.77, B:S.78, B:S.78, B:G.168, A:K.50 Water bridges: B:S.78, B:S.78 GOL.15: 2 residues within 4Å: Chain B: R.225, T.227 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.225, B:R.225, B:T.227, B:T.227, B:T.227 GOL.16: 3 residues within 4Å: Chain B: S.44, H.45, K.236 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.45, A:H.169

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 3 residues within 4Å: Chain A: S.44, H.45, K.236 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.44, A:H.45 SO4.8: 3 residues within 4Å: Chain A: N.183, F.185, R.213 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.183 Water bridges: A:R.213, A:R.213 Salt bridges: A:R.213 SO4.9: 2 residues within 4Å: Chain A: N.10, K.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.10 SO4.10: 2 residues within 4Å: Chain A: R.124, K.127 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.124

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 4 residues within 4Å: Chain A: M.17, K.41 Chain B: M.17, K.41 Ligand excluded by PLIP

1 x DD9: nonane(Non-covalent)

DD9.17: 3 residues within 4Å: Chain B: N.202, D.203, E.204 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.204

1 x D10: DECANE(Non-covalent)

D10.18: 8 residues within 4Å: Chain B: F.37, T.38, Y.154, I.166, A.205, H.233 Ligands: STE.12, GOL.13 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.154, B:I.166, B:A.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pinotsis, N. et al., Discovery of a non-canonical prototype long-chain monoacylglycerol lipase through a structure-based endogenous reaction intermediate complex. Nat Commun (2023)

Release Date

2023-05-10

Peptides

Serine aminopeptidase S33 domain-containing protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine aminopeptidase S33 domain-containing protein

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