Research workbench
Crystal structure of thermotoga maritima holo rimo in complex with pentasulfide, northeast structural genomics consortium target VR77
Analyse Crystal structure of thermotoga maritima holo rimo in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JC0
- Type
- protein
- Length
- 845 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal protein S12 methylthiotransferase rimo
- EC
- 2.-.-.-
- UniProt
- Q9X2H6
- Ligands
- FS5
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal protein S12 methylthiotransferase rimo (EC 2.-.-.-) | protein | 424 | 32% helix, 22% strand | Q9X2H6 |
| B | Ribosomal protein S12 methylthiotransferase rimo (EC 2.-.-.-) | protein | 421 | 31% helix, 22% strand | Q9X2H6 |
Ligands and binding sites
- FS5 · Iron/sulfur penta-sulfide connected clusters · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1193 | 0.83 | 0.84 | 99 | FS5 |
| 2 | 696 | 0.79 | 0.83 | 62 | FS5 |
| 3 | 213 | 0.61 | 0.82 | 32 | empty |
| 4 | 140 | 0.60 | 0.85 | 33 | empty |
| 5 | 127 | 0.47 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 584 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4JC0 · Crystal structure of Thermotoga maritima holo RimO in complex with pentasulfide… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X2H6 · AlphaFold monomer V2.0 prediction for ribosomal protein S12 methylthiotransferase rimo… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9X2H6
- Elsewhere: RCSB PDB 4JC0 · PDBe 4JC0 · UniProt Q9X2H6
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