SMTL ID : 3fgw.1

One chain form of the 66.3 kDa protein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 6 residues within 4Å: Chain A: L.25, G.30, N.69, S.71, F.161, T.163 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.25 NAG-NAG-BMA.16: 6 residues within 4Å: Chain B: L.25, G.30, N.69, S.71, F.161, T.163 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.25 Hydrogen bonds: B:T.163

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

NAG.2: 3 residues within 4Å: Chain A: K.113, A.188, N.190 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.188, A:N.190 NAG.3: 3 residues within 4Å: Chain A: E.391, N.395, Q.400 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.391 Hydrogen bonds: A:E.391, A:N.395 NAG.4: 5 residues within 4Å: Chain A: S.18, N.47, T.49, D.61, W.547 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.18, A:T.49 NAG.17: 3 residues within 4Å: Chain B: K.113, A.188, N.190 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.188, B:N.190 NAG.18: 3 residues within 4Å: Chain B: E.391, N.395, Q.400 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.391 Hydrogen bonds: B:E.391, B:E.391, B:N.395 NAG.19: 5 residues within 4Å: Chain B: S.18, N.47, T.49, D.61, W.547 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.18, B:T.49, B:T.49

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: V.368, F.390, E.391, T.392 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.392, A:T.392 Water bridges: A:E.391 GOL.6: 2 residues within 4Å: Chain A: E.247, Y.248 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.247 GOL.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.20: 4 residues within 4Å: Chain B: V.368, F.390, E.391, T.392 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.392 Water bridges: B:E.391 GOL.21: 2 residues within 4Å: Chain B: E.247, Y.248 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.247, B:E.247 GOL.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

14 x IOD: IODIDE ION(Non-functional Binders)

IOD.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: N.69, S.71 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain A: K.115, K.169, P.170, L.171 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: L.530, H.531 Ligand excluded by PLIP IOD.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.13: 1 residues within 4Å: Chain A: R.327 Ligand excluded by PLIP IOD.14: 4 residues within 4Å: Chain A: L.32, L.159, T.160, F.161 Ligand excluded by PLIP IOD.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.24: 2 residues within 4Å: Chain B: N.69, S.71 Ligand excluded by PLIP IOD.25: 4 residues within 4Å: Chain B: K.115, K.169, P.170, L.171 Ligand excluded by PLIP IOD.26: 2 residues within 4Å: Chain B: L.530, H.531 Ligand excluded by PLIP IOD.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.28: 1 residues within 4Å: Chain B: R.327 Ligand excluded by PLIP IOD.29: 4 residues within 4Å: Chain B: L.32, L.159, T.160, F.161 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.15: 6 residues within 4Å: Chain A: S.202, C.203, D.269, E.282, T.284, Y.333 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.284, A:Y.333 NA.30: 6 residues within 4Å: Chain B: S.202, C.203, D.269, E.282, T.284, Y.333 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.284, B:Y.333

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lakomek, K. et al., Initial insight into the function of the lysosomal 66.3 kDa protein from mouse by means of X-ray crystallography. Bmc Struct.Biol. (2009)

Release Date

2009-09-15

Peptides

Putative phospholipase B-like 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Putative phospholipase B-like 2

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