SMTL ID : 3fgr.1

Two chain form of the 66.3 kDa protein at 1.8 Angstroem

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

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: 7 residues within 4Å: Chain A: L.25, G.30, N.69, S.71, F.161, T.163 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.25 Water bridges: A:F.161 NAG-NAG.2: 3 residues within 4Å: Chain B: E.189, N.193, Q.198 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.198

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

NAG.3: 5 residues within 4Å: Chain A: K.113, A.188, L.189, N.190 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.189 Hydrogen bonds: A:K.113, A:A.188, A:N.190 NAG.4: 4 residues within 4Å: Chain A: N.47, T.49, Y.59, D.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.49 NAG.9: 1 residues within 4Å: Chain B: N.272 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.272 Water bridges: B:N.272

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: E.130, R.142, T.163, G.164, R.165 Ligands: NAG-NAG.1 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.126, A:E.130, A:R.142 GOL.6: 7 residues within 4Å: Chain A: N.99, Y.100, C.101, E.105, E.107, C.111, K.191 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.99, A:C.101, A:E.105, A:E.107, A:K.191 Water bridges: A:G.102 GOL.8: 7 residues within 4Å: Chain A: H.92, L.176, S.179 Chain B: N.22, N.26, Y.59, T.62 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:L.176, A:S.179, B:N.22, B:N.22, B:N.26, B:T.62 GOL.10: 7 residues within 4Å: Chain A: A.188, L.189 Chain B: W.91, K.92, V.94, Q.95 Ligands: NAG.3 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:A.188, B:Q.95 Hydrogen bonds: B:V.94 GOL.11: 5 residues within 4Å: Chain A: Y.137 Chain B: L.112, D.121, V.122, R.125 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:Y.137 Hydrogen bonds: B:R.125, B:R.125 GOL.12: 6 residues within 4Å: Chain A: E.183, D.184, P.187 Chain B: G.84, N.85, K.86 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.85, B:K.86, A:E.183, A:D.184 Water bridges: B:G.84 GOL.13: 3 residues within 4Å: Chain B: Y.187, F.188, E.189 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.189, B:E.189 Water bridges: B:K.170, B:Y.187, B:T.190 GOL.14: 6 residues within 4Å: Chain B: D.222, L.225, V.226, A.231, R.234, L.235 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.222, B:A.231, B:R.234, B:L.235 GOL.15: 7 residues within 4Å: Chain A: Q.147 Chain B: Y.34, L.36, F.38, I.63, V.107, R.111 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:I.63, B:R.111, B:R.111, A:Q.147 GOL.16: 9 residues within 4Å: Chain B: W.21, I.185, W.207, N.213, P.214, R.215, E.259, N.260, A.261 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:W.207, B:R.215, B:R.215, B:R.215, B:E.259, B:A.261 GOL.17: 3 residues within 4Å: Chain B: E.45, Y.46, P.47 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Y.46, B:Y.46

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

ACT.7: 4 residues within 4Å: Chain A: W.124, R.127, E.128, L.131 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.127, A:L.131 ACT.18: 5 residues within 4Å: Chain B: R.221, D.240, H.243, D.244, P.245 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.243 Water bridges: B:R.221 Salt bridges: B:R.221

1 x XE: XENON(Non-covalent)

XE.19: 5 residues within 4Å: Chain A: F.117, N.121 Chain B: C.99, L.101, S.128 No protein-ligand interaction detected (PLIP)

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

NA.20: 7 residues within 4Å: Chain A: S.200 Chain B: C.1, G.66, D.67, E.80, T.82, Y.131 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.80, B:Y.131, A:S.200

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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