MolNFT v1 · #164618 · protein
Pas-gaf fragment from deinococcus radiodurans phytochrome in dark state
6T3L · Bacteriophytochrome: “Pas-gaf fragment from deinococcus radiodurans phytochrome in dark state”. X-ray diffraction, 1 ligand (LBV), 8 pockets (best druggability 0.81). MolNFT v1 #164618 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6T3L
- Type
- protein
- Length
- 628 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriophytochrome
- EC
- 2.7.13.3
- UniProt
- Q9RZA4
- Ligands
- LBV
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Bacteriophytochrome (EC 2.7.13.3) | protein | 315 | 32% helix, 28% strand | Q9RZA4 |
| A | Bacteriophytochrome (EC 2.7.13.3) | protein | 313 | 32% 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 · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.81 | 0.87 | 75 | LBV |
| 2 | 312 | 0.79 | 0.89 | 42 | LBV |
| 3 | 246 | 0.64 | 0.82 | 34 | empty |
| 4 | 176 | 0.54 | 0.79 | 36 | empty |
| 5 | 156 | 0.53 | 0.80 | 38 | empty |
Interfaces
1 interface between chains.
- B–A · 1349 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (biliverdin attachment).
Compared structures
- 6T3L · PAS-GAF fragment from Deinococcus radiodurans phytochrome in dark state · the same entry in another collection · chain B against B, 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 6T3L · PDBe 6T3L · UniProt Q9RZA4
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