Research workbench
Crystal structure of a 8-amino-7-oxononanoate SYNTHASE/2-amino-3- ketobutyrate coenzyme a ligase from mycobacterium smegmatis
Analyse Crystal structure of a 8-amino-7-oxononanoate SYNTHASE/2-amino-3- ketobutyrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S5M
- Type
- protein
- Length
- 1,505 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 8-amino-7-oxononanoate synthase
- EC
- 2.3.1.47
- UniProt
- A0QX65
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 8-amino-7-oxononanoate synthase (EC 2.3.1.47) | protein | 377 | 45% helix, 16% strand | A0QX65 |
| B | 8-amino-7-oxononanoate synthase (EC 2.3.1.47) | protein | 378 | 44% helix, 16% strand | A0QX65 |
| C | 8-amino-7-oxononanoate synthase (EC 2.3.1.47) | protein | 379 | 44% helix, 16% strand | A0QX65 |
| D | 8-amino-7-oxononanoate synthase (EC 2.3.1.47) | protein | 371 | 44% helix, 16% strand | A0QX65 |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 963 | 0.86 | 0.88 | 121 | empty |
| 2 | 690 | 0.81 | 0.85 | 83 | empty |
| 3 | 1081 | 0.78 | 0.80 | 97 | empty |
| 4 | 940 | 0.78 | 0.80 | 93 | empty |
| 5 | 98 | 0.51 | 0.83 | 27 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3940 Ų buried · 59 hydrogen bonds · protein-protein
- C–D · 3863 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 410 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 233 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7S5M · Crystal Structure of a 8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A… · the same entry in another collection · chain D against D, TM-score 1.00
- A0QX65 · AlphaFold monomer V2.0 prediction for 8-amino-7-oxononanoate synthase (A0QX65) · a predicted model of the same protein · chain D 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 A0QX65
- Elsewhere: RCSB PDB 7S5M · PDBe 7S5M · UniProt A0QX65
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