Research workbench
2.95 ångström crystal structure of 16S rRNA methylase from proteus mirabilis
Analyse 2.95 ångström crystal structure of 16S rRNA methylase from proteus mirabilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CN0
- Type
- protein
- Length
- 1,058 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
- SO4, CL
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S rRNA (GUANINE(1405)-N(7))-methyltransferase (EC 2.1.1.179) | protein | 269 | 52% helix, 17% strand | Q33DX5 |
| B | 16S rRNA (GUANINE(1405)-N(7))-methyltransferase (EC 2.1.1.179) | protein | 272 | 49% helix, 17% strand | Q33DX5 |
| C | 16S rRNA (GUANINE(1405)-N(7))-methyltransferase (EC 2.1.1.179) | protein | 253 | 43% helix, 17% strand | Q33DX5 |
| D | 16S rRNA (GUANINE(1405)-N(7))-methyltransferase (EC 2.1.1.179) | protein | 264 | 50% helix, 18% strand | Q33DX5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains B
- CIT · Citric acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.84 | 0.84 | 89 | CIT |
| 2 | 1188 | 0.82 | 0.83 | 81 | SO4 |
| 3 | 477 | 0.74 | 0.83 | 44 | empty |
| 4 | 58 | 0.69 | 0.97 | 22 | empty |
| 5 | 319 | 0.68 | 0.82 | 48 | SO4 |
Interfaces
5 interfaces between chains.
- A–D · 1152 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1102 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 668 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 625 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 433 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6CN0 · 2.95 Angstrom Crystal Structure of 16S rRNA Methylase from Proteus mirabilis · 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 6CN0 · PDBe 6CN0 · UniProt Q33DX5
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