MolNFT v1 · #41225 · protein
The crystal structure of DR2241 from deinococcus radiodurans at 1.9 a resolution reveals a multi-domain protein with structural similarity to chelatases but also with two additional novel domains
2JH3 · Ribosomal protein S2-related protein: “The crystal structure of DR2241 from deinococcus radiodurans at 1.9 a resolution reveals a multi-domain…”. X-ray diffraction, 1 ligand (SF4), 20 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 2JH3
- Type
- protein
- Length
- 1,833 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal protein S2-related protein
- UniProt
- Q9RS86
- Ligands
- SF4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ribosomal protein S2-related protein | protein | 459 | 43% helix, 19% strand | Q9RS86 |
| D | Ribosomal protein S2-related protein | protein | 456 | 44% helix, 20% strand | Q9RS86 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.81 | 0.84 | 81 | empty |
| 2 | 698 | 0.79 | 0.84 | 78 | empty |
| 3 | 383 | 0.75 | 0.86 | 55 | SF4 |
| 4 | 420 | 0.75 | 0.84 | 64 | SF4 |
| 5 | 471 | 0.74 | 0.83 | 56 | SF4 |
Interfaces
4 interfaces between chains.
- A–C · 1187 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 1180 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 1131 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 974 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2JH3 · The crystal structure of DR2241 from Deinococcus radiodurans at 1.9 A resolution reveals… · 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 Q9RS86
- Elsewhere: RCSB PDB 2JH3 · PDBe 2JH3 · UniProt Q9RS86
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