SMTL ID : 6xs3.1 (1 other biounit)

X-ray structure of the monoclinic crystal form at 2.48 A resolution of lipase from Thermomyces (Humicola) lanuginosa at 298 K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

homo-trimer

Ligands

3 x OCA: OCTANOIC ACID (CAPRYLIC ACID)(Covalent)

OCA.1: 15 residues within 4Å: Chain A: Y.43, G.104, S.105, W.111, N.114, H.167, S.168, L.169, H.280, L.281, I.287, G.288, T.289 Chain B: L.115 Ligands: LTV.4 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.281, B:L.115 Hydrogen bonds: A:S.105, A:S.105, A:N.114, A:L.169 OCA.6: 13 residues within 4Å: Chain B: Y.43, G.104, S.105, N.114, H.167, S.168, L.169, H.280, L.281, G.288 Chain C: I.112, L.115 Ligands: LTV.9 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:I.112, C:L.115, B:Y.43 Hydrogen bonds: B:S.105, B:S.105, B:L.169 OCA.11: 12 residues within 4Å: Chain A: I.112, L.115 Chain C: Y.43, G.104, S.105, H.167, S.168, L.169, H.280, L.281, G.288 Ligands: LTV.14 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.43, C:L.281 Hydrogen bonds: C:S.105, C:S.105, C:L.169

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: N.55, E.67, A.69, D.70, A.71 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.67, A:A.69 CA.7: 6 residues within 4Å: Chain B: N.55, E.67, A.69, D.70, A.71 Ligands: NAG.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.67, B:A.69, H2O.5 CA.12: 6 residues within 4Å: Chain C: N.55, E.67, A.69, D.70, A.71 Ligands: NAG.13 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.67, C:A.69, H2O.6

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

NAG.3: 2 residues within 4Å: Chain A: N.55, D.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.55, A:D.70 NAG.8: 3 residues within 4Å: Chain B: N.55, D.70 Ligands: CA.7 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.55, B:N.55 NAG.13: 4 residues within 4Å: Chain C: N.55, A.69, D.70 Ligands: CA.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.55

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

LTV.4: 25 residues within 4Å: Chain A: S.105, W.111, N.114, L.115, F.117, H.132, F.135, S.168, L.169, P.196, V.225, L.228, P.229, P.230, E.232, F.233, I.277, H.280, L.281 Chain B: L.115 Chain C: T.248, D.276, I.277, P.278 Ligands: OCA.1 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:W.111, A:W.111, A:W.111, A:N.114, A:F.233, C:P.278 Hydrogen bonds: A:N.114 LTV.9: 28 residues within 4Å: Chain A: I.277, P.278 Chain B: S.105, R.106, W.111, N.114, L.115, H.132, F.135, S.168, L.169, P.196, I.224, V.225, L.228, P.229, P.230, F.233, I.274, P.275, I.277, H.280, L.281 Chain C: I.108, I.112, L.115 Ligands: OCA.6, LTV.14 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.111, B:I.224, B:V.225, B:L.228, B:P.275, B:I.277, B:I.277 LTV.14: 24 residues within 4Å: Chain A: I.112, L.115 Chain B: I.274, P.275, I.277, P.278 Chain C: S.105, R.106, W.111, N.114, L.115, H.132, F.135, S.168, L.169, P.196, I.224, V.225, L.228, P.229, F.233, I.277 Ligands: LTV.9, OCA.11 9 PLIP interactions: 6 interactions with chain C, 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: C:W.111, C:L.115, C:V.225, A:I.112, A:L.115, B:I.274 Hydrogen bonds: C:N.114, C:H.132, C:L.169

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

PO4.5: 5 residues within 4Å: Chain A: R.197, R.227, P.230, R.231, E.232 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.231, A:E.232 Water bridges: A:R.197, A:R.197, A:N.270 Salt bridges: A:R.197 PO4.10: 6 residues within 4Å: Chain B: E.78, D.79, D.84, T.86, R.103, S.107 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.78 Salt bridges: B:R.103

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. Current Enzyme Inhibition (2020)

Release Date

2020-10-14

Peptides

Lipase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
F

Lipase

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