MolNFT v1 · #80232 · protein
Structure of an ribosomal subunit interface protein from coxiella burnetii
3TQM · Ribosome-associated factor Y: “Structure of an ribosomal subunit interface protein from coxiella burnetii”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.78). MolNFT v1 #80232 on GenesisL1: 3D structure, binding…
- PDB
- 3TQM
- Type
- protein
- Length
- 369 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosome-associated factor Y
- UniProt
- Q83DI6
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosome-associated factor Y | protein | 91 | 37% helix, 36% strand | Q83DI6 |
| B | Ribosome-associated factor Y | protein | 92 | 38% helix, 36% strand | Q83DI6 |
| C, D | Ribosome-associated factor Y | protein | 93 | 38% helix, 38% strand | Q83DI6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.78 | 0.80 | 111 | empty |
| 2 | 120 | 0.51 | 0.81 | 23 | empty |
| 3 | 112 | 0.48 | 0.80 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–C · 526 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 525 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 214 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 213 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 146 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3TQM · Structure of an ribosomal subunit interface protein from Coxiella burnetii · the same entry in another collection · chain C against C, 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 Q83DI6
- Elsewhere: RCSB PDB 3TQM · PDBe 3TQM · UniProt Q83DI6
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