SMTL ID : 6nyq.1

Crystal structure of glycosylated lysosomal membrane protein (GLMP) luminal domain bound to a Fab fragment

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NA.1: 5 residues within 4Å: Chain B: S.7, G.8, D.10, L.20, T.113 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.8 NA.2: 7 residues within 4Å: Chain C: S.286, G.341, Y.342, D.344, Q.345, Y.346, Y.347 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.344, C:Q.345, C:Y.346, C:Y.347, C:Y.347 NA.3: 6 residues within 4Å: Chain C: L.74, G.75, P.76, A.78, S.314, I.316 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.74 NA.4: 6 residues within 4Å: Chain C: E.128, Y.148, S.224, P.225, R.226, F.232 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.148, C:Y.148

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

NAG.5: 3 residues within 4Å: Chain C: E.37, S.63, N.64 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:E.37, C:N.64 Water bridges: C:E.37, C:T.38, C:S.63, C:S.63, C:N.64 NAG.6: 3 residues within 4Å: Chain C: N.85, S.113, Q.116 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.85, C:Q.116 Water bridges: C:N.85, C:Q.116 NAG.7: 1 residues within 4Å: Chain C: N.94 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.94 NAG.8: 6 residues within 4Å: Chain C: S.47, P.52, Q.53, N.54, N.157, T.159 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:P.52 Hydrogen bonds: C:S.47, C:S.47 Water bridges: C:S.47, C:Q.53, C:Q.53, C:T.159 NAG.9: 1 residues within 4Å: Chain C: N.228 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.228 NAG.10: 8 residues within 4Å: Chain C: L.127, F.129, P.144, E.235, H.304, A.329, F.330, N.331 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:E.235, C:A.329 Hydrogen bonds: C:E.235 Water bridges: C:E.235

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manzanillo, P. et al., GLMP is essential for bone-marrow hematopoiesis and lysosomal glycolipid metabolism. To Be Published

Release Date

2020-01-22

Peptides

1H3 Fab light chain: A
1H3 Fab heavy chain: B
Glycosylated lysosomal membrane protein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
C

1H3 Fab light chain

1H3 Fab heavy chain

Glycosylated lysosomal membrane protein