Research workbench
Crystal structure of native phycocyanin from T. elongatus in spacegroup P21212 at 2.1 ångströms
Analyse Crystal structure of native phycocyanin from T. elongatus in spacegroup P21212… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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