MolNFT v1 · #57813 · protein
Crystal structure of pcya V225D-biliverdin IX alpha complex
3AJG · PHYCOCYANOBILIN:FERREDOXIN oxidoreductase: “Crystal structure of pcya V225D-biliverdin IX alpha complex”. X-ray diffraction, 1 ligand (BLA), 7 pockets (best druggability 0.75). MolNFT v1 #57813 on GenesisL1: 3D structure, binding…
- PDB
- 3AJG
- Type
- protein
- Length
- 479 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
- BLA
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PHYCOCYANOBILIN:FERREDOXIN oxidoreductase (EC 1.3.7.5) | protein | 238 | 38% helix, 26% strand | Q55891 |
| B | PHYCOCYANOBILIN:FERREDOXIN oxidoreductase (EC 1.3.7.5) | protein | 241 | 37% helix, 26% strand | Q55891 |
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
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 390 | 0.75 | 0.85 | 46 | BLA |
| 2 | 309 | 0.66 | 0.81 | 37 | BLA |
| 3 | 73 | 0.40 | 0.79 | 13 | empty |
| 4 | 100 | 0.33 | 0.73 | 18 | empty |
| 5 | 69 | 0.31 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 458 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3AJG · Crystal structure of PcyA V225D-biliverdin IX 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 3AJG · PDBe 3AJG · UniProt Q55891
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