MolNFT v1 · #147911 · protein
Crystal structure of a putative acetyltransferase from bacillus cereus species.
6ERD · Aminoglycoside N6'-acetyltransferase: “Crystal structure of a putative acetyltransferase from bacillus cereus species.”. X-ray diffraction, 1 ligand (CL), 5 pockets (best druggability 0.79). MolNFT v1 #147911 on GenesisL1: 3D…
- PDB
- 6ERD
- Type
- protein
- Length
- 662 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminoglycoside N6'-acetyltransferase
- EC
- 2.3.1.82
- UniProt
- Q81D84
- Ligands
- CL
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminoglycoside N6'-acetyltransferase (EC 2.3.1.82) | protein | 167 | 34% helix, 37% strand | Q81D84 |
| B | Aminoglycoside N6'-acetyltransferase (EC 2.3.1.82) | protein | 161 | 34% helix, 38% strand | Q81D84 |
| C | Aminoglycoside N6'-acetyltransferase (EC 2.3.1.82) | protein | 164 | 35% helix, 38% strand | Q81D84 |
| D | Aminoglycoside N6'-acetyltransferase (EC 2.3.1.82) | protein | 170 | 34% helix, 36% strand | Q81D84 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.79 | 0.81 | 99 | GOL |
| 2 | 990 | 0.79 | 0.80 | 90 | GOL, CL |
| 3 | 131 | 0.53 | 0.81 | 24 | empty |
| 4 | 94 | 0.37 | 0.76 | 17 | CL |
| 5 | 66 | 0.28 | 0.73 | 20 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1038 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1035 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 713 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 18 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 modified (engineered, artifact).
Compared structures
- 6ERD · Crystal structure of a putative acetyltransferase from Bacillus cereus species. · 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 Q81D84
- Elsewhere: RCSB PDB 6ERD · PDBe 6ERD · UniProt Q81D84
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