MolNFT v1 · #153790 · protein
Crystal structure of phycocyanin from nostoc sp. R76DM
6JPR: “Crystal structure of phycocyanin from nostoc sp. R76DM”. X-ray diffraction, 2 ligands (CYC, NA), 20 pockets (best druggability 0.83). MolNFT v1 #153790 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JPR
- Type
- protein
- Length
- 2,004 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phycocyanin
- Ligands
- CYC, NA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Phycocyanin | protein | 162 | 78% helix, 0% strand | — |
| B, D, F, H, J, L | Phycocyanin | protein | 172 | 74% helix, 0% strand | — |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 18 copies · chains A, F, B, G, C, D, K, E, I, L, H, J
- NA · Sodium ion · metal · 5 copies · chains A, H, I, B, D, E, K, F
- GOL · Glycerol · additive · 11 copies · chains B, G, C, D, E, H, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.83 | 0.92 | 40 | CYC |
| 2 | 316 | 0.82 | 0.92 | 38 | CYC |
| 3 | 306 | 0.82 | 0.92 | 37 | CYC |
| 4 | 301 | 0.81 | 0.92 | 38 | CYC |
| 5 | 294 | 0.81 | 0.91 | 37 | CYC |
Interfaces
30 interfaces between chains.
- A–B · 1691 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1672 Ų buried · 18 hydrogen bonds · protein-protein
- K–L · 1666 Ų buried · 17 hydrogen bonds · protein-protein
- I–J · 1662 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1650 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 cofactor, 6 modified (phycocyanobilin attachment, nonstandard).
Compared structures
- 6JPR · Crystal structure of Phycocyanin from Nostoc sp. R76DM · 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
- Elsewhere: RCSB PDB 6JPR · PDBe 6JPR
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.