Research workbench
R2F from corynebacterium ammoniagenes in its mn substituted form
Analyse R2F from corynebacterium ammoniagenes in its mn substituted form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KGP
- Type
- protein
- Length
- 1,184 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleotide reductase protein R2F
- UniProt
- O69274
- Ligands
- MN
- Pockets
- 12 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ribonucleotide reductase protein R2F | protein | 296 | 78% helix, 0% strand | O69274 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 10 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.56 | 0.83 | 21 | empty |
| 2 | 285 | 0.52 | 0.74 | 35 | empty |
| 3 | 136 | 0.42 | 0.75 | 18 | empty |
| 4 | 140 | 0.39 | 0.73 | 22 | empty |
| 5 | 73 | 0.37 | 0.77 | 17 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2758 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2755 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 241 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1KGP · R2F from Corynebacterium Ammoniagenes in its Mn substituted form · 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 1KGP · PDBe 1KGP · UniProt O69274
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