Research workbench
Crystal structure of aminoglycoside-resistance methyltransferase rmtc bound to S-adenosylhomocysteine (sah)
Analyse Crystal structure of aminoglycoside-resistance methyltransferase rmtc bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PQB
- Type
- protein
- Length
- 1,054 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S rRNA (GUANINE(1405)-N(7))-methyltransferase
- EC
- 2.1.1.179
- UniProt
- Q33DX5
- Ligands
- SAH
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S rRNA (GUANINE(1405)-N(7))-methyltransferase (EC 2.1.1.179) | protein | 263 | 46% helix, 19% strand | Q33DX5 |
| B | 16S rRNA (GUANINE(1405)-N(7))-methyltransferase (EC 2.1.1.179) | protein | 264 | 48% helix, 18% strand | Q33DX5 |
| C | 16S rRNA (GUANINE(1405)-N(7))-methyltransferase (EC 2.1.1.179) | protein | 266 | 45% helix, 19% strand | Q33DX5 |
| D | 16S rRNA (GUANINE(1405)-N(7))-methyltransferase (EC 2.1.1.179) | protein | 261 | 46% helix, 18% strand | Q33DX5 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.86 | 0.87 | 102 | SAH |
| 2 | 438 | 0.68 | 0.80 | 43 | empty |
| 3 | 185 | 0.67 | 0.86 | 32 | SAH |
| 4 | 301 | 0.65 | 0.81 | 44 | SAH |
| 5 | 319 | 0.63 | 0.79 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–B · 948 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 756 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 632 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 555 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 404 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6PQB · Crystal structure of aminoglycoside-resistance methyltransferase RmtC bound to… · the same entry in another collection · chain D against D, TM-score 1.00
- Q33DX5 · AlphaFold monomer V2.0 prediction for 16S rRNA (GUANINE(1405)-N(7))-methyltransferase… · a predicted model of the same protein · chain A 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 Q33DX5
- Elsewhere: RCSB PDB 6PQB · PDBe 6PQB · UniProt Q33DX5
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