SMTL ID : 6xrv.2 (1 other biounit)

X-ray structure of the monoclinic crystal form at 1.43 A resolution of lipase from Thermomyces (Humicola) lanuginosa at 173 K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-trimer

Ligands

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

OCA.1: 13 residues within 4Å: Chain A: Y.43, S.105, W.111, H.167, S.168, L.169, V.225, H.280, L.281, G.288 Chain C: I.112, L.115 Ligands: LTV.6 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:Y.43, A:W.111, A:W.111, A:L.281, C:L.115 Hydrogen bonds: A:S.105, A:L.169 OCA.8: 12 residues within 4Å: Chain A: L.115 Chain B: Y.43, G.104, S.105, W.111, N.114, H.167, S.168, L.169, H.280, L.281 Ligands: LTV.11 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:S.168, A:L.115 Hydrogen bonds: B:S.105, B:N.114, B:L.169 OCA.12: 12 residues within 4Å: Chain C: Y.43, G.104, S.105, N.114, H.167, S.168, L.169, V.225, H.280, L.281, G.288 Ligands: LTV.15 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.43, C:L.169 Hydrogen bonds: C:S.105

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

PO4.2: 6 residues within 4Å: Chain A: R.197, R.227, P.230, R.231, E.232, N.270 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.227, A:R.231, A:N.270 Water bridges: A:E.232, A:E.232 Salt bridges: A:R.197 PO4.7: 3 residues within 4Å: Chain A: K.120, E.121, R.130 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.121 Water bridges: A:R.130, A:R.130 Salt bridges: A:R.130 PO4.16: 3 residues within 4Å: Chain C: K.120, E.121, R.130 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.121 Salt bridges: C:R.130 PO4.17: 7 residues within 4Å: Chain C: R.197, R.227, P.230, R.231, E.232, N.270 Ligands: LTV.15 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.231, C:N.270 Salt bridges: C:R.197

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: N.55, E.67, A.69, D.70, A.71 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.67, A:A.69, H2O.5, H2O.6, H2O.9 CA.4: 3 residues within 4Å: Chain A: D.84, R.103, S.107 No protein-ligand interaction detected (PLIP) CA.9: 5 residues within 4Å: Chain B: N.55, E.67, A.69, D.70, A.71 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.67, B:A.69, H2O.16, H2O.17, H2O.19 CA.13: 5 residues within 4Å: Chain C: E.67, A.69, D.70, A.71 Ligands: NAG.14 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.67, C:A.69, H2O.25, H2O.25, H2O.25

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

NAG.5: 2 residues within 4Å: Chain A: N.55, D.70 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.55, A:D.70 Water bridges: A:N.55 NAG.10: 2 residues within 4Å: Chain B: N.55, D.70 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.55, B:D.70 Water bridges: B:N.55, B:D.70 NAG.14: 3 residues within 4Å: Chain C: N.55, D.70 Ligands: CA.13 6 PLIP interactions: 6 interactions with chain C Water bridges: C:N.55, C:N.55, C:N.55, C:A.69, C:D.70, C:A.71

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

LTV.6: 31 residues within 4Å: Chain A: S.105, R.106, 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, I.274, P.275, I.277, H.280, L.281 Chain B: I.277, P.278 Chain C: I.108, W.111, I.112, L.115 Ligands: OCA.1, LTV.11, LTV.15 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:W.111, A:W.111, A:W.111, A:L.115, A:I.224, A:L.228, A:P.275, A:I.277, C:I.108, C:I.112, C:L.115 Hydrogen bonds: A:L.169 LTV.11: 27 residues within 4Å: Chain A: I.108, I.112 Chain B: S.105, R.106, 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, I.274, P.275, I.277 Chain C: I.277, P.278 Ligands: LTV.6, OCA.8, LTV.15 11 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: B:W.111, B:W.111, B:I.224, B:V.225, B:I.277, C:I.277, C:P.278, A:I.112 Hydrogen bonds: B:H.132, B:S.168, B:L.169 LTV.15: 31 residues within 4Å: Chain A: I.277, P.278 Chain B: I.108, W.111, I.112, L.115 Chain C: S.105, R.106, I.108, W.111, N.114, L.115, F.117, H.132, F.135, P.196, I.224, V.225, R.227, L.228, P.229, P.230, F.233, N.273, P.275, I.277, H.280 Ligands: LTV.6, LTV.11, OCA.12, PO4.17 15 PLIP interactions: 9 interactions with chain C, 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: C:I.108, C:W.111, C:W.111, C:V.225, C:R.227, C:P.230, C:P.275, C:I.277, B:I.108, B:I.108, B:W.111, B:I.112, A:I.277, A:P.278 Hydrogen bonds: C:H.132

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
B

B
C

C
E

Lipase

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