MolNFT v1 · #175954 · protein
Crystal structure of phycocyanin from synechococcus sp. R42DM
7D6W · Phycocyanin alpha subunit: “Crystal structure of phycocyanin from synechococcus sp. R42DM”. X-ray diffraction, 1 ligand (CYC), 20 pockets (best druggability 0.84). MolNFT v1 #175954 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7D6W
- Type
- protein
- Length
- 2,004 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phycocyanin alpha subunit; Phycocyanin beta subunit
- Ligands
- CYC
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Phycocyanin alpha subunit | protein | 162 | 78% helix, 0% strand | — |
| B, D, F, H, J, L | Phycocyanin beta subunit | protein | 172 | 77% helix, 0% strand | — |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 18 copies · chains A, H, B, E, C, F, D, G, J, L, I, 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 | 1067 | 0.84 | 0.85 | 130 | CYC |
| 2 | 729 | 0.83 | 0.87 | 96 | CYC |
| 3 | 320 | 0.80 | 0.90 | 39 | CYC |
| 4 | 308 | 0.80 | 0.90 | 37 | CYC |
| 5 | 337 | 0.79 | 0.89 | 40 | CYC |
Interfaces
30 interfaces between chains.
- G–H · 1655 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1630 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1614 Ų buried · 12 hydrogen bonds · protein-protein
- K–L · 1582 Ų buried · 12 hydrogen bonds · protein-protein
- I–J · 1580 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 cofactor, 6 modified (phycocyanobilin attachment, nonstandard).
Compared structures
- 7D6W · Crystal structure of Phycocyanin from Synechococcus sp. R42DM · 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 7D6W · PDBe 7D6W
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