MolNFT v1 · #136616 · protein
Crystal structure of the dark-adapted full-length bacteriophytochrome xccbphp mutant D199A from xanthomonas campestris
5UYR: “Crystal structure of the dark-adapted full-length bacteriophytochrome xccbphp mutant D199A from xanthomonas…”. X-ray diffraction, 1 ligand (BLA), 18 pockets (best druggability 0.79). MolNFT v1 #136616 on GenesisL1: 3D structure…
- PDB
- 5UYR
- Type
- protein
- Length
- 1,197 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriophytochrome
- UniProt
- A0A0H2XCS3
- Ligands
- BLA
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriophytochrome | protein | 597 | 35% helix, 25% strand | A0A0H2XCS3 |
| B | Bacteriophytochrome | protein | 600 | 35% helix, 25% strand | A0A0H2XCS3 |
Ligands and binding sites
- BLA · Biliverdine IX alpha · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.79 | 0.89 | 39 | BLA |
| 2 | 585 | 0.78 | 0.84 | 79 | empty |
| 3 | 339 | 0.77 | 0.87 | 39 | BLA |
| 4 | 472 | 0.75 | 0.84 | 34 | empty |
| 5 | 482 | 0.72 | 0.82 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 3348 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (biliverdin attachment).
Compared structures
- 5UYR · Crystal structure of the dark-adapted full-length bacteriophytochrome XccBphP mutant… · 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 A0A0H2XCS3
- Elsewhere: RCSB PDB 5UYR · PDBe 5UYR · UniProt A0A0H2XCS3
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