Research workbench
Crystal structure of phormidium C-phycoerythrin at pH 5.0
Analyse Crystal structure of phormidium C-phycoerythrin at pH 5.0 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FVB
- Type
- protein
- Length
- 4,176 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-phycoerythrin alpha subunit; C-phycoerythrin beta subunit
- UniProt
- A0A0E3W010, A0A0E4G455
- Ligands
- PEB
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | C-phycoerythrin alpha subunit | protein | 164 | 77% helix, 0% strand | A0A0E3W010 |
| M, N, O, P, Q, R, S, T, U, V, W, X | C-phycoerythrin beta subunit | protein | 184 | 72% helix, 0% strand | A0A0E4G455 |
Ligands and binding sites
- PEB · Phycoerythrobilin · ligand · 60 copies · chains A, O, B, M, C, N, D, Q, E, R, F, P, G, U, H, S, I, T, J, W, K, X, L, V
- GOL · Glycerol · additive · 11 copies · chains A, M, B, N, C, O, D, P, E, G, S, H, T, I, U, J, V, K, L, X
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 | 960 | 0.89 | 0.90 | 130 | PEB |
| 2 | 1172 | 0.88 | 0.89 | 144 | PEB |
| 3 | 1186 | 0.87 | 0.88 | 131 | PEB |
| 4 | 1091 | 0.87 | 0.88 | 137 | PEB |
| 5 | 1049 | 0.87 | 0.88 | 126 | PEB |
Interfaces
61 interfaces between chains.
- J–V · 1495 Ų buried · 16 hydrogen bonds · protein-protein
- G–S · 1493 Ų buried · 15 hydrogen bonds · protein-protein
- H–T · 1491 Ų buried · 18 hydrogen bonds · protein-protein
- K–W · 1490 Ų buried · 17 hydrogen bonds · protein-protein
- D–P · 1487 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 cofactor, 12 modified (phycoerythrobilin attachment, nonstandard).
Compared structures
- 5FVB · Crystal structure of phormidium C-phycoerythrin at pH 5.0 · 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 A0A0E3W010
- Every structure of UniProt A0A0E4G455
- Elsewhere: RCSB PDB 5FVB · PDBe 5FVB · UniProt A0A0E3W010 · UniProt A0A0E4G455
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