Research workbench
Crystal structure of the B-phycoerythrin from the red algae porphyridium cruentum at PH8
Analyse Crystal structure of the B-phycoerythrin from the red algae porphyridium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V57
- Type
- protein
- Length
- 682 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phycoerythrin alpha subunit; Phycoerythrin beta subunit
- UniProt
- E2IH77, E2IH76
- Ligands
- PEB, SO4
- Pockets
- 17 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Phycoerythrin alpha subunit | protein | 164 | 78% helix, 0% strand | E2IH77 |
| B, D | Phycoerythrin beta subunit | protein | 177 | 74% helix, 0% strand | E2IH76 |
Ligands and binding sites
- PEB · Phycoerythrobilin · ligand · 10 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.64 | 0.90 | 23 | PEB |
| 2 | 92 | 0.63 | 0.89 | 23 | PEB |
| 3 | 223 | 0.60 | 0.80 | 40 | empty |
| 4 | 201 | 0.59 | 0.81 | 27 | empty |
| 5 | 80 | 0.57 | 0.87 | 14 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1603 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1603 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1047 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 332 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 324 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 cofactor, 2 modified (phycoerythrobilin attachment, nonstandard).
Compared structures
- 3V57 · Crystal Structure of the B-phycoerythrin from the red algae Porphyridium Cruentum at pH8 · 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 E2IH77
- Every structure of UniProt E2IH76
- Elsewhere: RCSB PDB 3V57 · PDBe 3V57 · UniProt E2IH77 · UniProt E2IH76
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