MolNFT v1 · #145730 · protein
X-ray crystal structure of flavobacterium johnsoniae DIMANGANESE(II) ribonucleotide reductase beta subunit (anaerobic)
6CWP: “X-ray crystal structure of flavobacterium johnsoniae DIMANGANESE(II) ribonucleotide reductase beta subunit…”. X-ray diffraction, 1 ligand (MN), 5 pockets (best druggability 0.70). MolNFT v1 #145730 on GenesisL1: 3D structure…
- PDB
- 6CWP
- Type
- protein
- Length
- 613 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleotide reductase; Val-glu-tyr-thr-lys-his
- UniProt
- A5FCJ5
- Ligands
- MN
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleotide reductase | protein | 300 | 73% helix, 0% strand | A5FCJ5 |
| B | Ribonucleotide reductase | protein | 307 | 69% helix, 1% strand | A5FCJ5 |
| F | Val-glu-tyr-thr-lys-his | protein | 6 | 0% helix, 33% strand | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.70 | 0.79 | 67 | empty |
| 2 | 372 | 0.63 | 0.78 | 39 | empty |
| 3 | 63 | 0.50 | 0.85 | 15 | empty |
| 4 | 63 | 0.33 | 0.76 | 15 | empty |
| 5 | 62 | 0.32 | 0.76 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1230 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 409 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 31 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6CWP · X-ray crystal structure of Flavobacterium johnsoniae dimanganese(II) ribonucleotide… · the same entry in another collection · chain B against B, 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 A5FCJ5
- Elsewhere: RCSB PDB 6CWP · PDBe 6CWP · UniProt A5FCJ5
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