MolNFT v1 · #83948 · protein
Crystal structure of mycobacterium smegmatis 7-keto-8-aminopelargonic acid (kapa) synthase biof
3WY7 · 8-amino-7-oxononanoate synthase: “Crystal structure of mycobacterium smegmatis 7-keto-8-aminopelargonic acid (kapa) synthase biof”. X-ray diffraction, 18 pockets (best druggability 0.76). MolNFT v1 #83948 on GenesisL1: 3D structure…
- PDB
- 3WY7
- Type
- protein
- Length
- 1,432 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
- 18 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 8-amino-7-oxononanoate synthase (EC 2.3.1.47) | protein | 346 | 42% helix, 18% strand | A0QX65 |
| B | 8-amino-7-oxononanoate synthase (EC 2.3.1.47) | protein | 369 | 42% helix, 16% strand | A0QX65 |
| D | 8-amino-7-oxononanoate synthase (EC 2.3.1.47) | protein | 371 | 43% helix, 16% strand | A0QX65 |
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 771 | 0.76 | 0.81 | 67 | empty |
| 2 | 1171 | 0.76 | 0.78 | 99 | empty |
| 3 | 850 | 0.76 | 0.80 | 71 | empty |
| 4 | 748 | 0.74 | 0.80 | 70 | empty |
| 5 | 561 | 0.64 | 0.76 | 60 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2701 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2653 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 227 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3WY7 · Crystal structure of Mycobacterium smegmatis 7-Keto-8-aminopelargonic acid (KAPA)… · 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 C against A, TM-score 0.98
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 3WY7 · PDBe 3WY7 · UniProt A0QX65
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