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Crystal structure of an aminoglycoside acetyltransferase HMB0005 from an uncultured soil metagenomic sample, unknown active site density modeled as polyethylene glycol
Analyse Crystal structure of an aminoglycoside acetyltransferase HMB0005 from an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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