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Crystal structure of adenosylmethionine-8-amino-7-oxononanoate aminotransferase from methanocaldococcus jannaschii dsm 2661
Analyse Crystal structure of adenosylmethionine-8-amino-7-oxononanoate aminotransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZHK
- Type
- protein
- Length
- 876 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
- Q58696
- Ligands
- MG
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 438 | 44% helix, 17% strand | Q58696 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.82 | 0.87 | 76 | empty |
| 2 | 704 | 0.80 | 0.84 | 74 | empty |
| 3 | 73 | 0.43 | 0.81 | 16 | empty |
| 4 | 71 | 0.40 | 0.80 | 16 | empty |
| 5 | 58 | 0.33 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 5766 Ų buried · 73 hydrogen bonds · protein-protein
Compared structures
- 6ZHK · Crystal structure of adenosylmethionine-8-amino-7-oxononanoate aminotransferase from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q58696 · AlphaFold monomer V2.0 prediction for adenosylmethionine-8-amino-7-oxononanoate… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q58696
- Elsewhere: RCSB PDB 6ZHK · PDBe 6ZHK · UniProt Q58696
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