Research workbench
Crystal structure of D. radiodurans bacteriophytochrome photosensory core module in its illuminated form
Analyse Crystal structure of D. radiodurans bacteriophytochrome photosensory core… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O01
- Type
- protein
- Length
- 1,934 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriophytochrome
- EC
- 2.7.13.3
- UniProt
- Q9RZA4
- Ligands
- LBV
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Bacteriophytochrome (EC 2.7.13.3) | protein | 483 | 36% helix, 23% strand | Q9RZA4 |
| B | Bacteriophytochrome (EC 2.7.13.3) | protein | 486 | 36% helix, 23% strand | Q9RZA4 |
| D | Bacteriophytochrome (EC 2.7.13.3) | protein | 482 | 36% helix, 23% 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 · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 607 | 0.82 | 0.87 | 78 | LBV |
| 2 | 405 | 0.81 | 0.90 | 49 | LBV |
| 3 | 386 | 0.80 | 0.89 | 43 | LBV |
| 4 | 385 | 0.80 | 0.89 | 46 | LBV |
| 5 | 390 | 0.70 | 0.82 | 32 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1415 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1390 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 495 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 439 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 cofactor (biliverdin attachment).
Compared structures
- 4O01 · Crystal Structure of D. radiodurans Bacteriophytochrome Photosensory Core Module in its… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9RZA4 · AlphaFold monomer V2.0 prediction for bacteriophytochrome (Q9RZA4) · a predicted model of the same protein · chain D against A, TM-score 0.86
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 4O01 · PDBe 4O01 · UniProt Q9RZA4
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