MolNFT v1 · #121148 · protein
Crystal structure of an aminoglycoside acetyltransferase HMB0005 from an uncultured soil metagenomic sample, unknown active site density modeled as polyethylene glycol
5HMN · AAC3-I: “Crystal structure of an aminoglycoside acetyltransferase HMB0005 from an uncultured soil metagenomic sample…”. X-ray diffraction, 1 ligand (COA), 6 pockets (best druggability 0.79). MolNFT v1 #121148 on GenesisL1: 3D…
- PDB
- 5HMN
- Type
- protein
- Length
- 918 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AAC3-I
- UniProt
- A0A059WV44
- Ligands
- COA
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | AAC3-I | protein | 151 | 42% helix, 35% strand | A0A059WV44 |
| B | AAC3-I | protein | 159 | 37% helix, 34% strand | A0A059WV44 |
| C | AAC3-I | protein | 152 | 37% helix, 34% strand | A0A059WV44 |
| D | AAC3-I | protein | 154 | 36% helix, 34% strand | A0A059WV44 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 5 copies · chains A, B, C, E, F
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.79 | 0.81 | 86 | empty |
| 2 | 1007 | 0.75 | 0.77 | 65 | COA |
| 3 | 536 | 0.70 | 0.79 | 42 | COA |
| 4 | 528 | 0.69 | 0.78 | 41 | COA |
| 5 | 474 | 0.67 | 0.78 | 43 | COA |
Interfaces
8 interfaces between chains.
- A–B · 3177 Ų buried · 60 hydrogen bonds · protein-protein
- D–F · 3141 Ų buried · 49 hydrogen bonds · protein-protein
- C–E · 3092 Ų buried · 52 hydrogen bonds · protein-protein
- D–E · 442 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 208 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5HMN · Crystal structure of an aminoglycoside acetyltransferase HMB0005 from an uncultured soil… · the same entry in another collection · chain A 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 A0A059WV44
- Elsewhere: RCSB PDB 5HMN · PDBe 5HMN · UniProt A0A059WV44
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