MolNFT v1 · #37295 · protein
Structure of archaeoglobus fulgidis xpb
2FWR · DNA repair protein RAD25: “Structure of archaeoglobus fulgidis xpb”. X-ray diffraction, 1 ligand (PO4), 15 pockets (best druggability 0.79). MolNFT v1 #37295 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2FWR
- Type
- protein
- Length
- 1,699 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair protein RAD25
- UniProt
- O29889
- Ligands
- PO4
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair protein RAD25 | protein | 434 | 33% helix, 20% strand | O29889 |
| B | DNA repair protein RAD25 | protein | 423 | 34% helix, 22% strand | O29889 |
| C | DNA repair protein RAD25 | protein | 414 | 33% helix, 20% strand | O29889 |
| D | DNA repair protein RAD25 | protein | 428 | 33% helix, 19% strand | O29889 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 8 copies · chains A, D, B, C
- IPA · Isopropyl alcohol · additive · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.79 | 0.81 | 83 | PO4, IPA |
| 2 | 803 | 0.78 | 0.82 | 82 | PO4 |
| 3 | 1057 | 0.74 | 0.77 | 72 | empty |
| 4 | 971 | 0.72 | 0.76 | 82 | empty |
| 5 | 584 | 0.63 | 0.74 | 51 | empty |
Interfaces
3 interfaces between chains.
- A–D · 664 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 656 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 316 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2FWR · Structure of Archaeoglobus Fulgidis XPB · 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 O29889
- Elsewhere: RCSB PDB 2FWR · PDBe 2FWR · UniProt O29889
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