MolNFT v1 · #49193 · protein
The udp complex structure of the sixth gene product of the F1-ATPase operon of rhodobacter blasticus
2QGI · ATP synthase subunits region orf 6: “The udp complex structure of the sixth gene product of the F1-ATPase operon of rhodobacter blasticus”. X-ray diffraction, 2 ligands (UDP, MN), 8 pockets (best druggability 0.74). MolNFT v1 #49193…
- PDB
- 2QGI
- Type
- protein
- Length
- 496 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunits region orf 6
- UniProt
- P05449
- Ligands
- UDP, MN
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATP synthase subunits region orf 6 | protein | 248 | 26% helix, 29% strand | P05449 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.74 | 0.97 | 15 | empty |
| 2 | 408 | 0.70 | 0.81 | 45 | empty |
| 3 | 418 | 0.66 | 0.79 | 41 | MN, UDP |
| 4 | 239 | 0.50 | 0.75 | 40 | empty |
| 5 | 158 | 0.46 | 0.76 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 2285 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 2QGI · The UDP complex structure of the sixth gene product of the F1-ATPase operon of… · the same entry in another collection · chain B against B, TM-score 1.00
- P05449 · AlphaFold monomer V2.0 prediction for ATP synthase subunits region orf 6 (P05449) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P05449
- Elsewhere: RCSB PDB 2QGI · PDBe 2QGI · UniProt P05449
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