MolNFT v1 · #171255 · protein
Crystal structure of native phycocyanin from T. elongatus in spacegroup P21212 at 2.1 ångströms
6YYJ · C-phycocyanin alpha chain: “Crystal structure of native phycocyanin from T. elongatus in spacegroup P21212 at 2.1 ångströms”. X-ray diffraction, 1 ligand (PXQ), 16 pockets (best druggability 0.75). MolNFT v1 #171255 on GenesisL1: 3D…
- PDB
- 6YYJ
- Type
- protein
- Length
- 1,002 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-phycocyanin alpha chain; C-phycocyanin beta chain
- UniProt
- P50032, P50033
- Ligands
- PXQ
- Pockets
- 16 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | C-phycocyanin alpha chain | protein | 162 | 78% helix, 0% strand | P50032 |
| B, D, F | C-phycocyanin beta chain | protein | 172 | 76% helix, 0% strand | P50033 |
Ligands and binding sites
- PXQ · 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(~{Z})-(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid · ligand · 9 copies · chains A, B, E, C, D, F
- PGE · Triethylene glycol · additive · 5 copies · chains A, E, F, C, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.75 | 0.78 | 96 | PXQ |
| 2 | 91 | 0.64 | 0.89 | 22 | PXQ |
| 3 | 82 | 0.63 | 0.89 | 21 | PXQ |
| 4 | 98 | 0.62 | 0.88 | 19 | PXQ |
| 5 | 211 | 0.58 | 0.80 | 28 | PGE |
Interfaces
8 interfaces between chains.
- A–B · 1646 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1626 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1613 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 937 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 691 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 covalent, 3 modified (covalent ligand, nonstandard).
Compared structures
- 6YYJ · Crystal structure of native Phycocyanin from T. elongatus in spacegroup P21212 at 2.1… · the same entry in another collection · chain F against F, TM-score 1.00
- P50032 · AlphaFold monomer V2.0 prediction for C-phycocyanin alpha subunit (P50032) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P50033 · AlphaFold monomer V2.0 prediction for C-phycocyanin beta subunit (P50033) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P50032
- Every structure of UniProt P50033
- Elsewhere: RCSB PDB 6YYJ · PDBe 6YYJ · UniProt P50032 · UniProt P50033
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