SMTL ID : 6o8v.1

The structure of lipase from Thermomyces Lanuginosa in complex with 1,3 diacylglycerol: Rhombohedral crystal form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-trimer

Ligands

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 3 residues within 4Å: Chain A: N.55, A.69, D.70 5 PLIP interactions: 5 interactions with chain A Water bridges: A:N.55, A:N.55, A:N.55, A:A.69, A:A.71 NAG.9: 3 residues within 4Å: Chain B: N.55, A.69, D.70 5 PLIP interactions: 5 interactions with chain B Water bridges: B:N.55, B:N.55, B:N.55, B:A.69, B:A.71 NAG.17: 3 residues within 4Å: Chain C: N.55, A.69, D.70 5 PLIP interactions: 5 interactions with chain C Water bridges: C:N.55, C:N.55, C:N.55, C:A.69, C:A.71

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 4 residues within 4Å: Chain A: K.120, E.121, N.123, R.140 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.120, A:E.121, A:N.123 Water bridges: A:E.121, A:G.128 PG4.10: 4 residues within 4Å: Chain B: K.120, E.121, N.123, R.140 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.120, B:E.121, B:N.123 Water bridges: B:E.121, B:G.128 PG4.18: 4 residues within 4Å: Chain C: K.120, E.121, N.123, R.140 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.120, C:E.121, C:N.123 Water bridges: C:E.121, C:G.128

15 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 2 residues within 4Å: Chain A: P.51, A.52 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.52 Water bridges: A:D.49, A:A.50 PO4.4: 2 residues within 4Å: Chain A: T.59, G.60 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.60 PO4.5: 3 residues within 4Å: Chain A: D.79, S.80, G.81 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.81 Water bridges: A:D.79, A:S.80, A:S.80 PO4.6: 5 residues within 4Å: Chain A: R.201, R.231, G.234, Y.235, S.236 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.235, A:Y.235 Water bridges: A:R.231, A:S.236 PO4.7: 1 residues within 4Å: Ligands: LTV.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.222 PO4.11: 2 residues within 4Å: Chain B: P.51, A.52 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.52 Water bridges: B:D.49, B:A.50 PO4.12: 2 residues within 4Å: Chain B: T.59, G.60 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.60 PO4.13: 3 residues within 4Å: Chain B: D.79, S.80, G.81 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.81 Water bridges: B:D.79, B:S.80, B:S.80 PO4.14: 5 residues within 4Å: Chain B: R.201, R.231, G.234, Y.235, S.236 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.235, B:Y.235 Water bridges: B:R.231, B:S.236 PO4.15: 1 residues within 4Å: Ligands: LTV.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.222 PO4.19: 2 residues within 4Å: Chain C: P.51, A.52 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.52 Water bridges: C:D.49, C:A.50 PO4.20: 2 residues within 4Å: Chain C: T.59, G.60 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.60 PO4.21: 3 residues within 4Å: Chain C: D.79, S.80, G.81 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.81 Water bridges: C:D.79, C:S.80, C:S.80 PO4.22: 5 residues within 4Å: Chain C: R.201, R.231, G.234, Y.235, S.236 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.235, C:Y.235 Water bridges: C:R.231, C:S.236 PO4.23: 1 residues within 4Å: Ligands: LTV.24 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.222

3 x LTV: 2-hydroxy-3-(octadecanoyloxy)propyl pentacosanoate(Non-covalent)

LTV.8: 30 residues within 4Å: Chain A: S.105, R.106, L.108, W.111, N.114, L.115, F.117, H.132, F.135, S.168, L.169, P.196, I.224, V.225, L.228, P.229, P.230, F.233, P.275, I.277, H.280, L.281 Chain B: P.275, I.277, P.278 Chain C: L.108, W.111, I.112, L.115 Ligands: PO4.7 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:W.111, A:L.115, A:I.224, A:V.225, A:I.277, C:L.108 Hydrogen bonds: A:L.169 Water bridges: A:S.168 LTV.16: 30 residues within 4Å: Chain A: L.108, W.111, I.112, L.115 Chain B: S.105, R.106, L.108, W.111, N.114, L.115, F.117, H.132, F.135, S.168, L.169, P.196, I.224, V.225, L.228, P.229, P.230, F.233, P.275, I.277, H.280, L.281 Chain C: P.275, I.277, P.278 Ligands: PO4.15 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.111, B:L.115, B:I.224, B:V.225, B:I.277, A:L.108 Hydrogen bonds: B:L.169 Water bridges: B:S.168 LTV.24: 30 residues within 4Å: Chain A: P.275, I.277, P.278 Chain B: L.108, W.111, I.112, L.115 Chain C: S.105, R.106, L.108, W.111, N.114, L.115, F.117, H.132, F.135, S.168, L.169, P.196, I.224, V.225, L.228, P.229, P.230, F.233, P.275, I.277, H.280, L.281 Ligands: PO4.23 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.111, C:L.115, C:I.224, C:V.225, C:I.277, B:L.108 Hydrogen bonds: C:L.169 Water bridges: C:S.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McPherson , A. et al., The Crystal Structures of Thermomyces (Humicola) Lanuginosa Lipase in Complex with Enzymatic Reactants. Curr Enzym Inhib (2020)

Release Date

2024-05-01

Peptides

Lipase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Lipase

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