MolNFT v1 · #125427 · protein
Wild-type pas-gaf fragment from deinococcus radiodurans bphp collected at lcls
5L8M · Bacteriophytochrome: “Wild-type pas-gaf fragment from deinococcus radiodurans bphp collected at lcls”. X-ray diffraction, 1 ligand (LBV), 4 pockets (best druggability 0.79). MolNFT v1 #125427 on GenesisL1: 3D structure, binding…
- PDB
- 5L8M
- Type
- protein
- Length
- 305 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriophytochrome
- EC
- 2.7.13.3
- UniProt
- Q9RZA4
- Ligands
- LBV
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriophytochrome (EC 2.7.13.3) | protein | 305 | 30% helix, 28% strand | Q9RZA4 |
Ligands and binding sites
- LBV · 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium-2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid · ligand · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.79 | 0.91 | 40 | LBV |
| 2 | 119 | 0.55 | 0.83 | 28 | empty |
| 3 | 62 | 0.42 | 0.82 | 15 | empty |
| 4 | 73 | 0.39 | 0.78 | 17 | empty |
Modifications
Observed in the structure: 1 cofactor (biliverdin attachment).
Compared structures
- 5L8M · Wild-type PAS-GAF fragment from Deinococcus radiodurans Bphp collected at LCLS · the same entry in another collection · chain A against A, TM-score 1.00
- Q9RZA4 · AlphaFold monomer V2.0 prediction for bacteriophytochrome (Q9RZA4) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9RZA4
- Elsewhere: RCSB PDB 5L8M · PDBe 5L8M · UniProt Q9RZA4
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