Research workbench
Two chain form of the 66.3 kda protein at 1.8 angstroem
Analyse Two chain form of the 66.3 kda protein at 1.8 angstroem in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FGR
- Type
- protein
- Length
- 524 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative phospholipase B-like 2 28 kda form; Putative phospholipase B-like 2 40 kda form
- EC
- 3.1.1.-
- UniProt
- Q3TCN2
- Ligands
- NAG, NA, XE
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative phospholipase B-like 2 28 kda form (EC 3.1.1.-) | protein | 180 | 50% helix, 17% strand | Q3TCN2 |
| B | Putative phospholipase B-like 2 40 kda form (EC 3.1.1.-) | protein | 344 | 28% helix, 26% strand | Q3TCN2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- NA · Sodium ion · metal · chains A, B
- XE · Xenon · ion · chains A, B
- GOL · Glycerol · additive · 11 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.72 | 0.80 | 64 | GOL |
| 2 | 136 | 0.42 | 0.76 | 27 | GOL |
| 3 | 89 | 0.39 | 0.77 | 18 | empty |
| 4 | 59 | 0.38 | 0.79 | 12 | empty |
| 5 | 51 | 0.29 | 0.75 | 9 | GOL |
Interfaces
1 interface between chains.
- A–B · 3130 Ų buried · 58 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan, 2 disulfide, 1 modified (N-glycosylation, disulfide, oxidation).
Compared structures
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 3FGR · PDBe 3FGR · UniProt Q3TCN2
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