Research workbench
Rabbit acyloxyacyl hydrolase (aoah), proteolytically processed, S262A mutant, with lps
Analyse Rabbit acyloxyacyl hydrolase (aoah), proteolytically processed, S262A mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W7B
- Type
- protein
- Length
- 1,012 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyloxyacyl hydrolase small subunit; Acyloxyacyl hydrolase large subunit
- EC
- 3.1.1.77
- UniProt
- O18823
- Ligands
- FTT, MYR, PA1, NAG, FUC, GCS, KDO, CA, PO4, SO4
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyloxyacyl hydrolase small subunit (EC 3.1.1.77) | protein | 94 | 62% helix, 0% strand | O18823 |
| C | Acyloxyacyl hydrolase large subunit (EC 3.1.1.77) | protein | 413 | 41% helix, 10% strand | O18823 |
| B | Acyloxyacyl hydrolase small subunit (EC 3.1.1.77) | protein | 93 | 62% helix, 0% strand | O18823 |
| D | Acyloxyacyl hydrolase large subunit (EC 3.1.1.77) | protein | 412 | 41% helix, 9% strand | O18823 |
Ligands and binding sites
- FTT · 3-hydroxy-tetradecanoic acid · ligand · 6 copies · chains A, C, B, D
- MYR · Myristic acid · ligand · 4 copies · chains A, C, B, D
- PA1 · 2-amino-2-deoxy-alpha-D-glucopyranose · ligand · 2 copies · chains A, C, B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, C, B, D
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, C, B, D
- GCS · 2-amino-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, C, B, D
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · 2 copies · chains D
- CA · Calcium ion · metal · 6 copies · chains C, D
- PO4 · Phosphate ion · ion · 4 copies · chains C, D
- SO4 · Sulfate ion · ion · 2 copies · chains C, D
- PEG · Di(hydroxyethyl)ether · additive · 16 copies · chains A, C, D
- PGE · Triethylene glycol · additive · 7 copies · chains A, C, D
- 1PE · Pentaethylene glycol · additive · 4 copies · chains C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.78 | 0.98 | 19 | PEG |
| 2 | 106 | 0.78 | 0.97 | 21 | PGE |
| 3 | 1112 | 0.78 | 0.79 | 89 | PA1, PEG, FTT, MYR, 1PE |
| 4 | 1176 | 0.78 | 0.79 | 97 | MES, FTT, MYR, 1PE, PO4 |
| 5 | 432 | 0.61 | 0.76 | 41 | PEG |
Interfaces
6 interfaces between chains.
- A–C · 1255 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 1215 Ų buried · 3 hydrogen bonds · protein-protein
- C–B · 274 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 271 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 66 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5W7B · Rabbit acyloxyacyl hydrolase (AOAH), proteolytically processed, S262A mutant, with LPS · the same entry in another collection · chain D against D, TM-score 1.00
- O18823 · AlphaFold monomer V2.0 prediction for acyloxyacyl hydrolase (O18823) · 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 O18823
- Elsewhere: RCSB PDB 5W7B · PDBe 5W7B · UniProt O18823
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