Research workbench
Plasmodium yoelii ribonucleotide reductase subunit R2 (PY03671)
Analyse Plasmodium yoelii ribonucleotide reductase subunit R2 (PY03671) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P1I
- Type
- protein
- Length
- 2,050 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleotide reductase, small chain
- UniProt
- Q7RIF3
- Ligands
- FE
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F, H | Ribonucleotide reductase, small chain | protein | 258 | 68% helix, 0% strand | Q7RIF3 |
| B | Ribonucleotide reductase, small chain | protein | 252 | 67% helix, 0% strand | Q7RIF3 |
| C | Ribonucleotide reductase, small chain | protein | 256 | 70% helix, 0% strand | Q7RIF3 |
| G | Ribonucleotide reductase, small chain | protein | 252 | 66% helix, 0% strand | Q7RIF3 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.82 | 0.82 | 113 | empty |
| 2 | 1099 | 0.81 | 0.82 | 124 | empty |
| 3 | 849 | 0.76 | 0.79 | 76 | empty |
| 4 | 769 | 0.75 | 0.80 | 76 | empty |
| 5 | 692 | 0.74 | 0.79 | 57 | empty |
Interfaces
7 interfaces between chains.
- G–H · 808 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 737 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 728 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 723 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 154 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2P1I · Plasmodium yoelii Ribonucleotide Reductase Subunit R2 (PY03671) · 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 Q7RIF3
- Elsewhere: RCSB PDB 2P1I · PDBe 2P1I · UniProt Q7RIF3
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