MolNFT v1 · #63510 · protein
Crystal structure of the lysosomal 66.3 kda protein from mouse solved by S-sad
3FBX · Putative phospholipase B-like 2: “Crystal structure of the lysosomal 66.3 kda protein from mouse solved by S-sad”. X-ray diffraction, 3 ligands (NAG, NA, XE), 6 pockets (best druggability 0.71). MolNFT v1 #63510 on GenesisL1: 3D…
- PDB
- 3FBX
- Type
- protein
- Length
- 520 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative phospholipase B-like 2
- EC
- 3.1.1.-
- UniProt
- Q3TCN2
- Ligands
- NAG, NA, XE
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative phospholipase B-like 2 (EC 3.1.1.-) | protein | 520 | 35% helix, 23% strand | Q3TCN2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- NA · Sodium ion · metal · chains A
- XE · Xenon · ion · chains A
- GOL · Glycerol · additive · 3 copies · chains A
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A
- ACT · Acetate ion · additive · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.71 | 0.79 | 61 | GOL |
| 2 | 114 | 0.40 | 0.76 | 21 | empty |
| 3 | 81 | 0.39 | 0.77 | 18 | empty |
| 4 | 57 | 0.37 | 0.79 | 12 | empty |
| 5 | 54 | 0.33 | 0.78 | 13 | empty |
Modifications
Observed in the structure: 4 glycan, 2 disulfide, 1 modified (N-glycosylation, disulfide, oxidation).
Compared structures
- 3FBX · Crystal structure of the lysosomal 66.3 kDa protein from mouse solved by S-SAD · the same entry in another collection · chain A against A, TM-score 1.00
- Q3TCN2 · AlphaFold monomer V2.0 prediction for putative phospholipase B-like 2 (Q3TCN2) · a predicted model of the same protein · chain A against A, 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 Q3TCN2
- Elsewhere: RCSB PDB 3FBX · PDBe 3FBX · UniProt Q3TCN2
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