Research workbench
Crystal structure of phycoerythrin
Analyse Crystal structure of phycoerythrin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B13
- Type
- protein
- Length
- 2,046 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phycoerythrin alpha subunit; Phycoerythrin beta subunit
- UniProt
- F2ZAL8, F2ZAL7
- Ligands
- CYC, PUB
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Phycoerythrin alpha subunit | protein | 164 | 78% helix, 0% strand | F2ZAL8 |
| G, H, I, J, K, L | Phycoerythrin beta subunit | protein | 177 | 74% helix, 0% strand | F2ZAL7 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 24 copies · chains A, K, G, C, B, L, H, D, E, J, F, I
- PUB · Phycourobilin · ligand · 6 copies · chains G, H, I, J, K, L
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 | 830 | 0.84 | 0.86 | 107 | CYC |
| 2 | 701 | 0.84 | 0.88 | 99 | empty |
| 3 | 858 | 0.84 | 0.86 | 125 | empty |
| 4 | 309 | 0.79 | 0.90 | 42 | CYC |
| 5 | 314 | 0.79 | 0.89 | 40 | CYC |
Interfaces
30 interfaces between chains.
- C–I · 1609 Ų buried · 20 hydrogen bonds · protein-protein
- A–G · 1606 Ų buried · 19 hydrogen bonds · protein-protein
- B–H · 1604 Ų buried · 21 hydrogen bonds · protein-protein
- D–J · 1604 Ų buried · 20 hydrogen bonds · protein-protein
- E–K · 1602 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 cofactor, 12 covalent (phycocyanobilin attachment, covalent ligand).
Compared structures
- 5B13 · Crystal structure of phycoerythrin · 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
- Every structure of UniProt F2ZAL8
- Every structure of UniProt F2ZAL7
- Elsewhere: RCSB PDB 5B13 · PDBe 5B13 · UniProt F2ZAL8 · UniProt F2ZAL7
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