SMTL ID : 3fgt.1

Two chain form of the 66.3 kDa protein from mouse lacking the linker peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-mer

Ligands

1 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: 6 residues within 4Å: Chain A: L.25, G.30, N.69, S.71, F.161, T.163 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.25 Water bridges: A:G.30

2 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:K.113, A:N.190 NAG.7: 2 residues within 4Å: Chain B: N.193, Q.198 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.193

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 1 residues within 4Å: Chain A: Y.90 No protein-ligand interaction detected (PLIP) ACT.6: 7 residues within 4Å: Chain A: N.99, Y.100, C.101, E.105, Y.110, C.111, K.191 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.100, A:Y.110 Hydrogen bonds: A:C.101 Salt bridges: A:K.191 ACT.8: 2 residues within 4Å: Chain B: P.9, T.178 6 PLIP interactions: 6 interactions with chain B Water bridges: B:K.6, B:G.10, B:G.10, B:G.11, B:T.178, B:T.178

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: R.53, E.54 Chain B: M.337, F.338 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.53 Water bridges: A:E.54 GOL.9: 7 residues within 4Å: Chain B: W.21, N.184, W.207, R.215, E.259, R.283, H.285 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.184, B:R.215, B:E.259, B:R.283, B:R.283 Water bridges: B:S.266 GOL.10: 9 residues within 4Å: Chain B: R.265, D.267, L.268, P.316, F.317, Q.318, K.321, S.322, P.323 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.316, B:Q.318 GOL.12: 6 residues within 4Å: Chain B: L.225, A.231, R.234, L.235, Y.238 Ligands: 7PE.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.231 Water bridges: B:R.234, B:R.234, B:Q.313 GOL.13: 3 residues within 4Å: Chain B: E.45, Y.46, P.47 No protein-ligand interaction detected (PLIP)

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

PG4.5: 10 residues within 4Å: Chain A: E.119, L.122, E.123, Q.126, L.145, F.166, T.167, I.168, K.169, P.170 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.123, A:Q.126, A:I.168 PG4.11: 10 residues within 4Å: Chain B: G.73, S.74, G.75, Y.140, K.141, F.143, L.144, P.145, F.295, K.299 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.73 Water bridges: B:K.299

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

NA.14: 6 residues within 4Å: Chain B: C.1, G.66, D.67, E.80, T.82, Y.131 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.80, B:T.82

1 x 7PE: 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL(Non-functional Binders)

7PE.15: 7 residues within 4Å: Chain B: R.221, D.222, R.234, Y.238, D.244, Q.313 Ligands: GOL.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.234 Water bridges: B:Y.238, B:Q.313

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 28 kDa form: A
Putative phospholipase B-like 2 40 kDa form: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative phospholipase B-like 2 28 kDa form

Putative phospholipase B-like 2 40 kDa form

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