Research workbench
Crystal structure of pcya V225D-biliverdin xiii alpha complex
Analyse Crystal structure of pcya V225D-biliverdin xiii alpha complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AJH
- Type
- protein
- Length
- 481 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PHYCOCYANOBILIN:FERREDOXIN oxidoreductase
- EC
- 1.3.7.5
- UniProt
- Q55891
- Ligands
- BL3
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PHYCOCYANOBILIN:FERREDOXIN oxidoreductase (EC 1.3.7.5) | protein | 240 | 38% helix, 25% strand | Q55891 |
| B | PHYCOCYANOBILIN:FERREDOXIN oxidoreductase (EC 1.3.7.5) | protein | 241 | 37% helix, 24% strand | Q55891 |
Ligands and binding sites
- BL3 · 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(3-ethenyl-4-methyl-5-oxo-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-2-ylidene]methy l]-5-[(Z)-(3-ethenyl-4-methyl-5-oxo-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 358 | 0.73 | 0.84 | 38 | BL3 |
| 2 | 385 | 0.72 | 0.83 | 50 | BL3 |
| 3 | 161 | 0.51 | 0.78 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 431 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3AJH · Crystal structure of PcyA V225D-biliverdin XIII alpha complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q55891 · AlphaFold monomer V2.0 prediction for PHYCOCYANOBILIN:FERREDOXIN oxidoreductase (Q55891) · 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 Q55891
- Elsewhere: RCSB PDB 3AJH · PDBe 3AJH · UniProt Q55891
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