SMTL ID : 3fbx.1

Crystal structure of the lysosomal 66.3 kDa protein from mouse solved by S-SAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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: 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:F.161 NAG-NAG.14: 6 residues within 4Å: Chain B: L.25, G.30, N.69, S.71, F.161, T.163 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.25 Hydrogen bonds: B:T.163 Water bridges: B:F.161

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

NAG.2: 3 residues within 4Å: Chain A: K.113, N.190 Ligands: PG4.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.113, A:N.190 NAG.3: 2 residues within 4Å: Chain A: N.395, Q.400 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.395 Water bridges: A:E.391 NAG.4: 1 residues within 4Å: Chain A: N.474 No protein-ligand interaction detected (PLIP) NAG.15: 3 residues within 4Å: Chain B: K.113, N.190 Ligands: PG4.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.113, B:N.190 NAG.16: 2 residues within 4Å: Chain B: N.395, Q.400 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.395 Water bridges: B:E.391 NAG.17: 1 residues within 4Å: Chain B: N.474 No protein-ligand interaction detected (PLIP)

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

PG4.5: 11 residues within 4Å: Chain A: K.113, N.116, F.117, A.188, L.189, W.293, K.294, V.296, Q.297, P.298 Ligands: NAG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.117, A:Q.297 PG4.6: 10 residues within 4Å: Chain A: D.317, G.318, A.319, A.322, D.323, K.326, R.355, T.358, V.369, D.371 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.317, A:G.318, A:A.319, A:K.326, A:K.326, A:D.371 PG4.18: 11 residues within 4Å: Chain B: K.113, N.116, F.117, A.188, L.189, W.293, K.294, V.296, Q.297, P.298 Ligands: NAG.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.117, B:Q.297 PG4.19: 10 residues within 4Å: Chain B: D.317, G.318, A.319, A.322, D.323, K.326, R.355, T.358, V.369, D.371 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.317, B:G.318, B:A.319, B:K.326, B:K.326

2 x XE: XENON(Non-covalent)

XE.7: 6 residues within 4Å: Chain A: F.117, N.121, Q.297, C.301, L.303, S.330 No protein-ligand interaction detected (PLIP) XE.20: 6 residues within 4Å: Chain B: F.117, N.121, Q.297, C.301, L.303, S.330 No protein-ligand interaction detected (PLIP)

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain A: Y.137, L.314, D.323, V.324, R.327 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.323, A:R.327 Water bridges: A:Y.137 GOL.10: 7 residues within 4Å: Chain A: H.92, L.176, S.179, N.224, N.228, Y.261, T.264 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.179, A:N.224, A:N.228, A:T.264, A:T.264 Water bridges: A:S.179, A:G.268 GOL.11: 5 residues within 4Å: Chain A: D.424, L.427, A.433, R.436, L.437 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.424, A:R.436 Water bridges: A:D.424, A:D.424 GOL.21: 5 residues within 4Å: Chain B: Y.137, L.314, D.323, V.324, R.327 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.323, B:R.327 Water bridges: B:Y.137 GOL.23: 7 residues within 4Å: Chain B: H.92, L.176, S.179, N.224, N.228, Y.261, T.264 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.179, B:N.224, B:N.228, B:T.264 Water bridges: B:T.96, B:T.96, B:S.179, B:G.268 GOL.24: 5 residues within 4Å: Chain B: D.424, L.427, A.433, R.436, L.437 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.424, B:R.436 Water bridges: B:D.424, B:D.424

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

ACT.9: 5 residues within 4Å: Chain A: C.101, G.102, E.105, V.108, C.111 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.101 ACT.22: 5 residues within 4Å: Chain B: C.101, G.102, E.105, V.108, C.111 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.101

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.12: 10 residues within 4Å: Chain A: Q.147, Y.236, L.238, F.240, G.253, L.256, Y.272, V.309, N.312, R.313 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.147, A:Y.272, A:R.313 PGE.25: 10 residues within 4Å: Chain B: Q.147, Y.236, L.238, F.240, G.253, L.256, Y.272, V.309, N.312, R.313 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.147, B:Y.272, B:Y.272, B:R.313

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

NA.13: 5 residues within 4Å: Chain A: C.203, D.269, E.282, T.284, Y.333 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.333, A:Y.333 NA.26: 5 residues within 4Å: Chain B: C.203, D.269, E.282, T.284, Y.333 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.282, B:T.284

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lakomek, K. et al., De novo sulfur SAD phasing of the lysosomal 66.3 kDa protein from mouse. Acta Crystallogr.,Sect.D (2009)

Release Date

2009-03-03

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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