MolNFT v1 · #175467 · protein
Aminoglycoside 2'-N-acetyltransferase from mycolicibacterium smegmatis-apo structure
7CRM: “Aminoglycoside 2'-N-acetyltransferase from mycolicibacterium smegmatis-apo structure”. X-ray diffraction, 17 pockets (best druggability 0.72). MolNFT v1 #175467 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7CRM
- Type
- protein
- Length
- 748 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminoglycoside 2'-N-acetyltransferase
- EC
- 2.3.1.-
- UniProt
- P94968
- Pockets
- 17 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminoglycoside 2'-N-acetyltransferase (EC 2.3.1.-) | protein | 189 | 24% helix, 33% strand | P94968 |
| B | Aminoglycoside 2'-N-acetyltransferase (EC 2.3.1.-) | protein | 186 | 27% helix, 35% strand | P94968 |
| C | Aminoglycoside 2'-N-acetyltransferase (EC 2.3.1.-) | protein | 184 | 26% helix, 33% strand | P94968 |
| D | Aminoglycoside 2'-N-acetyltransferase (EC 2.3.1.-) | protein | 189 | 28% helix, 37% strand | P94968 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.72 | 0.76 | 79 | empty |
| 2 | 410 | 0.64 | 0.78 | 39 | empty |
| 3 | 458 | 0.62 | 0.76 | 44 | EDO |
| 4 | 233 | 0.54 | 0.77 | 30 | empty |
| 5 | 260 | 0.52 | 0.75 | 30 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1305 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1250 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 376 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 83 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7CRM · Aminoglycoside 2'-N-acetyltransferase from Mycolicibacterium smegmatis-APO Structure · the same entry in another collection · chain D against D, TM-score 1.00
- P94968 · AlphaFold monomer V2.0 prediction for aminoglycoside 2'-N-acetyltransferase (P94968) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P94968
- Elsewhere: RCSB PDB 7CRM · PDBe 7CRM · UniProt P94968
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