Research workbench
Pad-1 in the absence of substrate
Analyse Pad-1 in the absence of substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VRX
- Type
- protein
- Length
- 1,431 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase
- UniProt
- A0A6J4AG16
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminotransferase | protein | 359 | 38% helix, 17% strand | A0A6J4AG16 |
| B | Aminotransferase | protein | 352 | 38% helix, 16% strand | A0A6J4AG16 |
| C | Aminotransferase | protein | 363 | 38% helix, 16% strand | A0A6J4AG16 |
| D | Aminotransferase | protein | 357 | 38% helix, 17% strand | A0A6J4AG16 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.76 | 0.99 | 29 | empty |
| 2 | 419 | 0.76 | 0.85 | 55 | SO4 |
| 3 | 933 | 0.76 | 0.79 | 103 | empty |
| 4 | 73 | 0.75 | 0.99 | 20 | empty |
| 5 | 70 | 0.75 | 0.99 | 19 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2884 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 2813 Ų buried · 57 hydrogen bonds · protein-protein
- A–C · 505 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 441 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 126 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 7VRX · Pad-1 in the absence of substrate · 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 A0A6J4AG16
- Elsewhere: RCSB PDB 7VRX · PDBe 7VRX · UniProt A0A6J4AG16
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