Research workbench
A. fulgidus lipase with fatty acid fragment and magnesium
Analyse A. fulgidus lipase with fatty acid fragment and magnesium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZYR
- Type
- protein
- Length
- 918 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipase, putative
- EC
- 3.1.1.3
- UniProt
- O28511
- Ligands
- MG
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipase, putative (EC 3.1.1.3) | protein | 464 | 29% helix, 31% strand | O28511 |
| B | Lipase, putative (EC 3.1.1.3) | protein | 454 | 28% helix, 29% strand | O28511 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.84 | 0.97 | 50 | 1PE |
| 2 | 216 | 0.84 | 0.97 | 46 | 1PE |
| 3 | 1058 | 0.81 | 0.82 | 103 | empty |
| 4 | 69 | 0.69 | 0.95 | 18 | empty |
| 5 | 265 | 0.66 | 0.82 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 914 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2ZYR · A. Fulgidus lipase with fatty acid fragment and magnesium · 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 O28511
- Elsewhere: RCSB PDB 2ZYR · PDBe 2ZYR · UniProt O28511
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