Research workbench
Murine core lysosomal multienzyme complex (lmc) composed of acid beta- galactosidase (GLB1) and protective protein cathepsin a (ppca, ctsa)
Analyse Murine core lysosomal multienzyme complex (lmc) composed of acid beta… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KDV
- Type
- protein
- Length
- 6,312 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase; Lysosomal protective protein
- EC
- 3.2.1.23, 3.4.16.5
- UniProt
- P23780, P16675
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 2 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Beta-galactosidase (EC 3.2.1.23) | protein | 600 | 23% helix, 28% strand | P23780 |
| B, D, F, H, J, L | Lysosomal protective protein (EC 3.4.16.5) | protein | 452 | 32% helix, 22% strand | P16675 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 66 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.79 | 0.82 | 85 | empty |
| 2 | 814 | 0.77 | 0.81 | 73 | empty |
| 3 | 558 | 0.76 | 0.83 | 50 | empty |
| 4 | 566 | 0.75 | 0.82 | 55 | empty |
| 5 | 575 | 0.75 | 0.82 | 53 | empty |
Interfaces
12 interfaces between chains.
- H–J · 1966 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 1960 Ų buried · 15 hydrogen bonds · protein-protein
- B–L · 1951 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 900 Ų buried · 0 hydrogen bonds · protein-protein
- E–G · 897 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 36 disulfide (N-glycosylation, disulfide).
Compared structures
- 7KDV · Murine core lysosomal multienzyme complex (LMC) composed of acid beta-galactosidase… · the same entry in another collection · chain L against L, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P23780
- Every structure of UniProt P16675
- Elsewhere: RCSB PDB 7KDV · PDBe 7KDV · UniProt P23780 · UniProt P16675
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