SMTL ID : 5gw8.1

Crystal structure of a putative DAG-like lipase (MgMDL2) from Malassezia globosa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 8 residues within 4Å: Chain A: A.234, N.235, D.261, D.262, E.264, G.265, S.275, L.276 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.261 NAG-NAG.2: 7 residues within 4Å: Chain B: A.234, N.235, D.261, D.262, E.264, G.265, L.276 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.261, B:E.264

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

NAG.3: 2 residues within 4Å: Chain A: N.84, S.87 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.84, A:S.87 NAG.7: 3 residues within 4Å: Chain B: N.84, S.87, S.275 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.84, B:S.86, B:S.86, B:S.87, B:S.275

2 x MLA: MALONIC ACID(Non-covalent)

MLA.4: 8 residues within 4Å: Chain A: R.184, P.217, R.218, A.219, R.256 Chain B: R.218, A.219 Ligands: MLA.9 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.218, A:A.219 Salt bridges: A:R.184, A:R.256 Water bridges: B:R.218 MLA.9: 8 residues within 4Å: Chain A: R.218, A.219 Chain B: R.184, P.217, R.218, A.219, R.256 Ligands: MLA.4 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.218, B:A.219 Water bridges: B:R.184, B:T.214, B:R.256 Salt bridges: B:R.184, B:R.256

4 x ACY: ACETIC ACID(Non-functional Binders)

ACY.5: 4 residues within 4Å: Chain A: Y.20, N.21, K.176, H.203 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.21 Salt bridges: A:K.176, A:H.203 ACY.10: 5 residues within 4Å: Chain B: L.88, L.92, Q.96, G.119, L.154 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.92, B:Q.96 ACY.11: 4 residues within 4Å: Chain B: Y.20, N.21, K.176, H.203 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.21 Water bridges: B:Y.178 Salt bridges: B:K.176, B:H.203 ACY.12: 2 residues within 4Å: Chain B: K.136, R.169 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.136, B:R.169

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.6: 3 residues within 4Å: Chain A: F.132, K.136, R.169 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.136, A:K.136, A:R.169 FMT.13: 2 residues within 4Å: Chain B: H.6, N.187 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.187 Water bridges: B:N.187

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain B: A.57, G.58, R.63 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.58, B:R.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lan, D. et al., Malassezia globosa MgMDL2 lipase: Crystal structure and rational modification of substrate specificity. Biochem. Biophys. Res. Commun. (2017)

Release Date

2017-09-27

Peptides

Hypothetical secretory lipase (Family 3): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hypothetical secretory lipase (Family 3)