MolNFT v1 · #153364 · protein
Crystal structure of the purple chromoprotein of stichodactyla haddoni with a glu-tyr-gly tri-peptide chromophore
6JC6 · Shcp: “Crystal structure of the purple chromoprotein of stichodactyla haddoni with a glu-tyr-gly tri-peptide…”. X-ray diffraction, 1 ligand (BJO), 20 pockets (best druggability 0.84). MolNFT v1 #153364 on GenesisL1: 3D structure…
- PDB
- 6JC6
- Type
- protein
- Length
- 1,757 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shcp
- Ligands
- BJO
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Shcp | protein | 220 | 6% helix, 56% strand | — |
| B | Shcp | protein | 221 | 6% helix, 56% strand | — |
| E, F, G, H | Shcp | protein | 219 | 6% helix, 57% strand | — |
Ligands and binding sites
- BJO · (4Z)-4-amino-4-{1-(carboxymethyl)-5-oxo-4-[(4-oxocyclohexa-2,5-dien-1-ylidene)methyl]-1,5-dihydro-2H-imidazol-2-ylidene}butanoic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
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 | 1050 | 0.84 | 0.85 | 106 | empty |
| 2 | 1198 | 0.83 | 0.85 | 112 | empty |
| 3 | 84 | 0.77 | 0.99 | 27 | BJO |
| 4 | 78 | 0.76 | 0.99 | 25 | BJO |
| 5 | 87 | 0.76 | 0.98 | 24 | BJO |
Interfaces
14 interfaces between chains.
- B–D · 1642 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1581 Ų buried · 20 hydrogen bonds · protein-protein
- E–G · 1566 Ų buried · 20 hydrogen bonds · protein-protein
- F–H · 1475 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 874 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 covalent (covalent ligand).
Compared structures
- 6JC6 · Crystal structure of the purple chromoprotein of Stichodactyla haddoni with a Glu-Tyr-Gly… · the same entry in another collection · chain C against C, 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
- Elsewhere: RCSB PDB 6JC6 · PDBe 6JC6
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