SMTL ID : 6or3.2 (1 other biounit)

Structure of an Acyl Intermediate of Thermomyces Lanuginosa Lipase With Palmitic Acid in an Orthorhombic Crystal

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 1 residues within 4Å: Chain A: D.49 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.49, H2O.1, H2O.1, H2O.6, H2O.6 CA.4: 1 residues within 4Å: Chain B: D.49 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.49, H2O.7, H2O.8, H2O.13, H2O.13 CA.7: 1 residues within 4Å: Chain C: D.49 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.49, H2O.14, H2O.15, H2O.19, H2O.20 CA.10: 1 residues within 4Å: Chain D: D.49 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.49, H2O.21, H2O.21, H2O.26, H2O.26

4 x PLM: PALMITIC ACID(Covalent)

PLM.2: 19 residues within 4Å: Chain A: G.104, 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, F.233 Chain D: I.224, L.228 Ligands: PLM.11 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.111, A:N.114, A:F.117, A:F.117, A:F.135, A:P.229, A:F.233 Hydrogen bonds: A:S.105, A:S.105, A:L.169 PLM.5: 19 residues within 4Å: Chain B: G.104, 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, F.233 Chain C: I.224, L.228 Ligands: PLM.8 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.111, B:N.114, B:F.117, B:F.117, B:F.135, B:P.229, B:F.233 Hydrogen bonds: B:S.105, B:S.105, B:L.169 PLM.8: 19 residues within 4Å: Chain B: I.224, L.228 Chain C: G.104, 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, F.233 Ligands: PLM.5 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:W.111, C:N.114, C:F.117, C:F.117, C:F.135, C:P.229, C:F.233 Hydrogen bonds: C:S.105, C:S.105, C:L.169 PLM.11: 19 residues within 4Å: Chain A: I.224, L.228 Chain D: G.104, 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, F.233 Ligands: PLM.2 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:W.111, D:N.114, D:F.117, D:F.117, D:F.135, D:P.229, D:F.233 Hydrogen bonds: D:S.105, D:S.105, D:L.169

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

NAG.3: 5 residues within 4Å: Chain A: N.55, E.67, K.68, A.69, D.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.55, A:K.68 NAG.6: 5 residues within 4Å: Chain B: N.55, E.67, K.68, A.69, D.70 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.55, B:K.68 NAG.9: 5 residues within 4Å: Chain C: N.55, E.67, K.68, A.69, D.70 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.55, C:K.68 NAG.12: 5 residues within 4Å: Chain D: N.55, E.67, K.68, A.69, D.70 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.55, D:K.68

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

2020-05-20

Peptides

Lipase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Lipase

Related Entries With Identical Sequence