MolNFT v1 · #138061 · protein
Human acyloxyacyl hydrolase (aoah), proteolytically processed, S263A mutant, with lps
5W7C: “Human acyloxyacyl hydrolase (aoah), proteolytically processed, S263A mutant, with lps”. X-ray diffraction, 4 ligands (FTT, DAO, NAG), 11 pockets (best druggability 0.78). MolNFT v1 #138061 on GenesisL1: 3D structure, binding sites…
- PDB
- 5W7C
- Type
- protein
- Length
- 1,061 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyloxyacyl hydrolase
- EC
- 3.1.1.77
- UniProt
- P28039
- Ligands
- FTT, DAO, NAG, CA
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acyloxyacyl hydrolase (EC 3.1.1.77) | protein | 111 | 68% helix, 0% strand | P28039 |
| C | Acyloxyacyl hydrolase (EC 3.1.1.77) | protein | 420 | 40% helix, 10% strand | P28039 |
| D | Acyloxyacyl hydrolase (EC 3.1.1.77) | protein | 419 | 39% helix, 10% strand | P28039 |
Ligands and binding sites
- FTT · 3-hydroxy-tetradecanoic acid · ligand · 6 copies · chains A, C, B, D
- DAO · Lauric acid · ligand · 2 copies · chains C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains C, D, A, B
- CA · Calcium ion · metal · 6 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.78 | 0.99 | 18 | empty |
| 2 | 91 | 0.78 | 0.98 | 18 | empty |
| 3 | 742 | 0.76 | 0.80 | 71 | FTT, DAO |
| 4 | 731 | 0.75 | 0.80 | 71 | FTT, DAO |
| 5 | 470 | 0.61 | 0.75 | 42 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1189 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 1179 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 68 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 5W7C · Human acyloxyacyl hydrolase (AOAH), proteolytically processed, S263A mutant, with LPS · the same entry in another collection · chain D against D, TM-score 1.00
- P28039 · AlphaFold monomer V2.0 prediction for acyloxyacyl hydrolase (P28039) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P28039
- Elsewhere: RCSB PDB 5W7C · PDBe 5W7C · UniProt P28039
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