MolNFT v1 · #39958 · protein
Structural characterization of a blue chromoprotein and its yellow mutant from the sea anemone cnidopus japonicus
2IB5 · Chromo protein: “Structural characterization of a blue chromoprotein and its yellow mutant from the sea anemone cnidopus…”. X-ray diffraction, 2 ligands (CRQ, PO4), 20 pockets (best druggability 0.86). MolNFT v1 #39958 on GenesisL1…
- PDB
- 2IB5
- Type
- protein
- Length
- 1,800 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromo protein
- UniProt
- A0AQQ7
- Ligands
- CRQ, PO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Chromo protein | protein | 225 | 5% helix, 56% strand | A0AQQ7 |
Ligands and binding sites
- CRQ · [2-(3-carbamoyl-1-imino-propyl)-4-(4-hydroxy-benzylidene)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- PO4 · Phosphate ion · ion · 16 copies · chains A, C, D, B, E, H, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 860 | 0.86 | 0.88 | 100 | PO4 |
| 2 | 470 | 0.83 | 0.90 | 48 | PO4 |
| 3 | 1015 | 0.81 | 0.82 | 110 | empty |
| 4 | 94 | 0.77 | 0.98 | 28 | CRQ |
| 5 | 88 | 0.76 | 0.98 | 30 | CRQ |
Interfaces
19 interfaces between chains.
- B–C · 1900 Ų buried · 27 hydrogen bonds · protein-protein
- E–H · 1896 Ų buried · 24 hydrogen bonds · protein-protein
- F–G · 1883 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1843 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 1144 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 modified, 16 cofactor (engineered, chromophore).
Compared structures
- 2IB5 · Structural characterization of a blue chromoprotein and its yellow mutant from the sea… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0AQQ7
- Elsewhere: RCSB PDB 2IB5 · PDBe 2IB5 · UniProt A0AQQ7
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