Research workbench
Structure of the RNA-processing inhibitor rraa from thermus thermophilis
Analyse Structure of the RNA-processing inhibitor rraa from thermus thermophilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J3L
- Type
- protein
- Length
- 974 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Demethylmenaquinone methyltransferase
- EC
- 2.1.1.-
- UniProt
- P83846
- Ligands
- MG, CL
- Pockets
- 14 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Demethylmenaquinone methyltransferase (EC 2.1.1.-) | protein | 164 | 16% helix, 35% strand | P83846 |
| C | Demethylmenaquinone methyltransferase (EC 2.1.1.-) | protein | 161 | 17% helix, 35% strand | P83846 |
| F | Demethylmenaquinone methyltransferase (EC 2.1.1.-) | protein | 157 | 16% helix, 32% strand | P83846 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.71 | 0.75 | 106 | empty |
| 2 | 270 | 0.46 | 0.72 | 35 | empty |
| 3 | 77 | 0.43 | 0.81 | 15 | CL |
| 4 | 64 | 0.39 | 0.81 | 19 | empty |
| 5 | 103 | 0.39 | 0.76 | 17 | empty |
Interfaces
11 interfaces between chains.
- D–F · 628 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 615 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 609 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 600 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 593 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 1J3L · Structure of the RNA-processing inhibitor RraA from Thermus thermophilis · 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
- Every structure of UniProt P83846
- Elsewhere: RCSB PDB 1J3L · PDBe 1J3L · UniProt P83846
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