SMTL ID : 3o0d.1 (6 other biounits)

Crystal structure of Lip2 lipase from Yarrowia lipolytica at 1.7 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

NAG.1: 8 residues within 4Å: Chain A: N.113, Y.137, G.141, D.145, N.174, L.175, N.178, H.180 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.137 Hydrogen bonds: A:N.113, A:D.145, A:D.145, A:N.174, A:N.178 NAG.2: 5 residues within 4Å: Chain A: L.110, A.112, I.130, N.134, N.138 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.130 Hydrogen bonds: A:L.110, A:N.138 Water bridges: A:L.110, A:N.134

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 3 residues within 4Å: Chain A: F.237, L.279, Q.282 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.279 Water bridges: A:Q.282 MPD.4: 2 residues within 4Å: Chain A: H.9, I.10 No protein-ligand interaction detected (PLIP) MPD.5: 4 residues within 4Å: Chain A: E.13, S.14, F.17, V.216 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.17 Hydrogen bonds: A:S.14

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.6: 3 residues within 4Å: Chain A: R.228, D.251, Q.281 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.228

1 x K: POTASSIUM ION(Non-covalent)

K.7: 5 residues within 4Å: Chain A: L.169, Q.189, V.192, H.243, C.244 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bordes, F. et al., Exploring the conformational states and rearrangements of Yarrowia lipolytica Lipase. Biophys.J. (2010)

Release Date

2010-11-24

Peptides

Triacylglycerol lipase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Triacylglycerol lipase

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