MolNFT v1 · #95732 · protein
Crystal structure of an acetate kinase from mycobacterium avium bound to an unknown acid-apcpp conjugate and manganese
4IZ9: “Crystal structure of an acetate kinase from mycobacterium avium bound to an unknown acid-apcpp conjugate and…”. X-ray diffraction, 2 ligands (APC, MN), 5 pockets (best druggability 0.66). MolNFT v1 #95732 on GenesisL1: 3D structure…
- PDB
- 4IZ9
- Type
- protein
- Length
- 381 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetate kinase
- EC
- 2.7.2.1
- UniProt
- A0QLU8
- Ligands
- APC, MN
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetate kinase (EC 2.7.2.1) | protein | 381 | 41% helix, 18% strand | A0QLU8 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
- SIN · Succinic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.66 | 0.79 | 44 | MN, SIN, EDO |
| 2 | 137 | 0.42 | 0.75 | 18 | empty |
| 3 | 66 | 0.40 | 0.80 | 20 | empty |
| 4 | 87 | 0.35 | 0.75 | 16 | APC |
| 5 | 51 | 0.32 | 0.77 | 17 | empty |
Compared structures
- 4IZ9 · Crystal structure of an acetate kinase from Mycobacterium avium bound to an unknown… · the same entry in another collection · chain A against A, TM-score 1.00
- A0QLU8 · AlphaFold monomer V2.0 prediction for acetate kinase (A0QLU8) · a predicted model of the same protein · chain A 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 A0QLU8
- Elsewhere: RCSB PDB 4IZ9 · PDBe 4IZ9 · UniProt A0QLU8
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