MolNFT v1 · #21122 · protein
Crystal structure of the D147N mutant of 7,8-diaminopelargonic acid synthase
1S08 · Adenosylmethionine-8-amino-7-oxononanoate aminotransferase: “Crystal structure of the D147N mutant of 7,8-diaminopelargonic acid synthase”. X-ray diffraction, 1 ligand (NA), 4 pockets (best druggability 0.68). MolNFT v1 #21122 on…
- PDB
- 1S08
- Type
- protein
- Length
- 821 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
- EC
- 2.6.1.62
- UniProt
- P12995
- Ligands
- NA
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 411 | 40% helix, 20% strand | P12995 |
| B | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 410 | 40% helix, 20% strand | P12995 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.68 | 0.87 | 40 | empty |
| 2 | 363 | 0.66 | 0.80 | 45 | empty |
| 3 | 57 | 0.49 | 0.86 | 18 | empty |
| 4 | 198 | 0.47 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 4399 Ų buried · 61 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 1S08 · Crystal Structure of the D147N Mutant of 7,8-Diaminopelargonic Acid Synthase · the same entry in another collection · chain A against A, TM-score 1.00
- P12995 · AlphaFold monomer V2.0 prediction for adenosylmethionine-8-amino-7-oxononanoate… · a predicted model of the same protein · chain B 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 P12995
- Elsewhere: RCSB PDB 1S08 · PDBe 1S08 · UniProt P12995
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.