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A protein coordinated tri-nuclear fe complex formed during soaking of crystals of the ribonucleotide reductase R2F protein from corynebacterium ammoniagenes
Analyse A protein coordinated tri-nuclear fe complex formed during soaking of crystals… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OQU
- Type
- protein
- Length
- 1,190 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleotide reductase subunit R2F
- UniProt
- O69274
- Ligands
- FE, OXY
- Pockets
- 10 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Ribonucleotide reductase subunit R2F | protein | 296 | 78% helix, 0% strand | O69274 |
| C | Ribonucleotide reductase subunit R2F | protein | 302 | 76% helix, 0% strand | O69274 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 20 copies · chains A, B, C, D
- OXY · Oxygen molecule · ion · 3 copies · chains A, C, D
- ACT · Acetate ion · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 327 | 0.55 | 0.74 | 44 | empty |
| 2 | 268 | 0.51 | 0.74 | 41 | empty |
| 3 | 87 | 0.51 | 0.83 | 22 | empty |
| 4 | 102 | 0.36 | 0.75 | 24 | empty |
| 5 | 63 | 0.35 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2754 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2740 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 292 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1OQU · A protein coordinated tri-nuclear Fe complex formed during soaking of crystals of the… · 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 O69274
- Elsewhere: RCSB PDB 1OQU · PDBe 1OQU · UniProt O69274
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