MolNFT v1 · #74862 · protein
Crystal structure of a gdsl-like lipase (BDI_0976) from parabacteroides distasonis atcc 8503 at 1.93 a resolution
3P94: “Crystal structure of a gdsl-like lipase (BDI_0976) from parabacteroides distasonis atcc 8503 at 1.93 a…”. X-ray diffraction, 3 pockets (best druggability 0.80). MolNFT v1 #74862 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3P94
- Type
- protein
- Length
- 809 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gdsl-like lipase
- UniProt
- A6LAN0
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Gdsl-like lipase | protein | 204 | 45% helix, 15% strand | A6LAN0 |
| C | Gdsl-like lipase | protein | 200 | 47% helix, 16% strand | A6LAN0 |
| D | Gdsl-like lipase | protein | 201 | 46% helix, 15% strand | A6LAN0 |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.80 | 0.82 | 76 | empty |
| 2 | 57 | 0.31 | 0.76 | 17 | empty |
| 3 | 55 | 0.30 | 0.76 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1017 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1007 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 213 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 194 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 57 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3P94 · Crystal structure of a GDSL-like Lipase (BDI_0976) from Parabacteroides distasonis ATCC… · the same entry in another collection · 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 A6LAN0
- Elsewhere: RCSB PDB 3P94 · PDBe 3P94 · UniProt A6LAN0
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