Research workbench
Crystal structure of the aminoglycoside resistance methyltransferase NPMB1
Analyse Crystal structure of the aminoglycoside resistance methyltransferase NPMB1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EHF
- Type
- protein
- Length
- 206 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S rRNA methyltransferase
- Ligands
- NA, CL
- Pockets
- 4 · best druggability 0.37
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S rRNA methyltransferase | protein | 206 | 37% helix, 27% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.37 | 0.80 | 13 | EDO |
| 2 | 51 | 0.34 | 0.79 | 18 | EDO |
| 3 | 68 | 0.31 | 0.75 | 21 | empty |
| 4 | 52 | 0.27 | 0.74 | 12 | empty |
Compared structures
- 7EHF · Crystal structure of the aminoglycoside resistance methyltransferase NpmB1 · 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
- Elsewhere: RCSB PDB 7EHF · PDBe 7EHF
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