Research workbench
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
Analyse The crystal structure of DR2241 from deinococcus radiodurans at 1.9 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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