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

X-ray structure of the rhombohedral form of the lipase from Thermomyces lanuginosa at 1.3 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-hexamer

Ligands

6 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.10: 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.19: 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 NAG.28: 3 residues within 4Å: Chain D: N.55, A.69, D.70 5 PLIP interactions: 5 interactions with chain D Water bridges: D:N.55, D:N.55, D:N.55, D:A.69, D:A.71 NAG.37: 3 residues within 4Å: Chain E: N.55, A.69, D.70 5 PLIP interactions: 5 interactions with chain E Water bridges: E:N.55, E:N.55, E:N.55, E:A.69, E:A.71 NAG.46: 3 residues within 4Å: Chain F: N.55, A.69, D.70 5 PLIP interactions: 5 interactions with chain F Water bridges: F:N.55, F:N.55, F:N.55, F:A.69, F:A.71

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

PG4.2: 4 residues within 4Å: Chain A: K.120, E.121, N.123, R.130 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.120, A:E.121, A:N.123 PG4.11: 4 residues within 4Å: Chain B: K.120, E.121, N.123, R.130 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.120, B:E.121, B:N.123 PG4.20: 4 residues within 4Å: Chain C: K.120, E.121, N.123, R.130 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.120, C:E.121, C:N.123 PG4.29: 4 residues within 4Å: Chain D: K.120, E.121, N.123, R.130 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.120, D:E.121, D:N.123 PG4.38: 4 residues within 4Å: Chain E: K.120, E.121, N.123, R.130 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.120, E:E.121, E:N.123 PG4.47: 4 residues within 4Å: Chain F: K.120, E.121, N.123, R.130 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:K.120, F:E.121, F:N.123

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

PO4.3: 2 residues within 4Å: Chain A: P.51, A.52 Ligand excluded by PLIP PO4.4: 2 residues within 4Å: Chain A: T.59, G.60 Ligand excluded by PLIP PO4.5: 3 residues within 4Å: Chain A: D.79, S.80, G.81 Ligand excluded by PLIP PO4.6: 8 residues within 4Å: Chain A: R.201, R.231, G.234, Y.235, S.236 Chain E: W.243, V.258, I.260 Ligand excluded by PLIP PO4.7: 1 residues within 4Å: Chain A: K.96 Ligand excluded by PLIP PO4.8: 2 residues within 4Å: Ligands: LTV.9, LTV.45 Ligand excluded by PLIP PO4.12: 2 residues within 4Å: Chain B: P.51, A.52 Ligand excluded by PLIP PO4.13: 2 residues within 4Å: Chain B: T.59, G.60 Ligand excluded by PLIP PO4.14: 3 residues within 4Å: Chain B: D.79, S.80, G.81 Ligand excluded by PLIP PO4.15: 8 residues within 4Å: Chain B: R.201, R.231, G.234, Y.235, S.236 Chain D: W.243, V.258, I.260 Ligand excluded by PLIP PO4.16: 1 residues within 4Å: Chain B: K.96 Ligand excluded by PLIP PO4.17: 2 residues within 4Å: Ligands: LTV.18, LTV.36 Ligand excluded by PLIP PO4.21: 2 residues within 4Å: Chain C: P.51, A.52 Ligand excluded by PLIP PO4.22: 2 residues within 4Å: Chain C: T.59, G.60 Ligand excluded by PLIP PO4.23: 3 residues within 4Å: Chain C: D.79, S.80, G.81 Ligand excluded by PLIP PO4.24: 8 residues within 4Å: Chain C: R.201, R.231, G.234, Y.235, S.236 Chain F: W.243, V.258, I.260 Ligand excluded by PLIP PO4.25: 1 residues within 4Å: Chain C: K.96 Ligand excluded by PLIP PO4.26: 2 residues within 4Å: Ligands: LTV.27, LTV.54 Ligand excluded by PLIP PO4.30: 2 residues within 4Å: Chain D: P.51, A.52 Ligand excluded by PLIP PO4.31: 2 residues within 4Å: Chain D: T.59, G.60 Ligand excluded by PLIP PO4.32: 3 residues within 4Å: Chain D: D.79, S.80, G.81 Ligand excluded by PLIP PO4.33: 8 residues within 4Å: Chain B: W.243, V.258, I.260 Chain D: R.201, R.231, G.234, Y.235, S.236 Ligand excluded by PLIP PO4.34: 1 residues within 4Å: Chain D: K.96 Ligand excluded by PLIP PO4.35: 2 residues within 4Å: Ligands: LTV.18, LTV.36 Ligand excluded by PLIP PO4.39: 2 residues within 4Å: Chain E: P.51, A.52 Ligand excluded by PLIP PO4.40: 2 residues within 4Å: Chain E: T.59, G.60 Ligand excluded by PLIP PO4.41: 3 residues within 4Å: Chain E: D.79, S.80, G.81 Ligand excluded by PLIP PO4.42: 8 residues within 4Å: Chain A: W.243, V.258, I.260 Chain E: R.201, R.231, G.234, Y.235, S.236 Ligand excluded by PLIP PO4.43: 1 residues within 4Å: Chain E: K.96 Ligand excluded by PLIP PO4.44: 2 residues within 4Å: Ligands: LTV.9, LTV.45 Ligand excluded by PLIP PO4.48: 2 residues within 4Å: Chain F: P.51, A.52 Ligand excluded by PLIP PO4.49: 2 residues within 4Å: Chain F: T.59, G.60 Ligand excluded by PLIP PO4.50: 3 residues within 4Å: Chain F: D.79, S.80, G.81 Ligand excluded by PLIP PO4.51: 8 residues within 4Å: Chain C: W.243, V.258, I.260 Chain F: R.201, R.231, G.234, Y.235, S.236 Ligand excluded by PLIP PO4.52: 1 residues within 4Å: Chain F: K.96 Ligand excluded by PLIP PO4.53: 2 residues within 4Å: Ligands: LTV.27, LTV.54 Ligand excluded by PLIP

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

LTV.9: 32 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: PO4.8, PO4.44, LTV.45 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:W.111, A:L.115, A:V.225, A:I.277, C:L.108 Hydrogen bonds: A:L.169 LTV.18: 32 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: PO4.17, PO4.35, LTV.36 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.111, B:L.115, B:V.225, B:I.277, A:L.108 Hydrogen bonds: B:L.169 LTV.27: 32 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: PO4.26, PO4.53, LTV.54 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.111, C:L.115, C:V.225, C:I.277, B:L.108 Hydrogen bonds: C:L.169 LTV.36: 32 residues within 4Å: Chain D: 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 E: P.275, I.277, P.278 Chain F: L.108, W.111, I.112, L.115 Ligands: PO4.17, LTV.18, PO4.35 6 PLIP interactions: 1 interactions with chain F, 5 interactions with chain D Hydrophobic interactions: F:L.108, D:W.111, D:L.115, D:V.225, D:I.277 Hydrogen bonds: D:L.169 LTV.45: 32 residues within 4Å: Chain D: L.108, W.111, I.112, L.115 Chain E: 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 F: P.275, I.277, P.278 Ligands: PO4.8, LTV.9, PO4.44 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:W.111, E:L.115, E:V.225, E:I.277, D:L.108 Hydrogen bonds: E:L.169 LTV.54: 32 residues within 4Å: Chain D: P.275, I.277, P.278 Chain E: L.108, W.111, I.112, L.115 Chain F: 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: PO4.26, LTV.27, PO4.53 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:W.111, F:L.115, F:V.225, F:I.277, E:L.108 Hydrogen bonds: F:L.169

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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Lipase

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