Research workbench
GH3.15 acyl acid amido synthetase
Analyse GH3.15 acyl acid amido synthetase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AVH
- Type
- protein
- Length
- 2,189 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GH3.15 acyl acid amido synthetase
- EC
- 6.-.-.-
- UniProt
- Q8GZ29
- Ligands
- AMP
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GH3.15 acyl acid amido synthetase (EC 6.-.-.-) | protein | 547 | 42% helix, 21% strand | Q8GZ29 |
| B | GH3.15 acyl acid amido synthetase (EC 6.-.-.-) | protein | 541 | 42% helix, 21% strand | Q8GZ29 |
| C | GH3.15 acyl acid amido synthetase (EC 6.-.-.-) | protein | 552 | 42% helix, 22% strand | Q8GZ29 |
| D | GH3.15 acyl acid amido synthetase (EC 6.-.-.-) | protein | 549 | 41% helix, 21% strand | Q8GZ29 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1115 | 0.85 | 0.86 | 89 | AMP |
| 2 | 1193 | 0.85 | 0.86 | 95 | AMP |
| 3 | 1164 | 0.83 | 0.84 | 98 | AMP |
| 4 | 1135 | 0.82 | 0.83 | 89 | AMP |
| 5 | 978 | 0.80 | 0.81 | 88 | empty |
Interfaces
6 interfaces between chains.
- B–C · 543 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 533 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 392 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 353 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 208 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
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 Q8GZ29
- Elsewhere: RCSB PDB 6AVH · PDBe 6AVH · UniProt Q8GZ29
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