MolNFT v1 · #96171 · protein
Crystal structure of thermotoga maritima holo rimo in complex with pentasulfide, northeast structural genomics consortium target VR77
4JC0 · Ribosomal protein S12 methylthiotransferase rimo: “Crystal structure of thermotoga maritima holo rimo in complex with pentasulfide, northeast structural…”. X-ray diffraction, 1 ligand (FS5), 12 pockets (best druggability 0.83).…
- 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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