MolNFT v1 · #5987 · protein
Crystal structure of R-phycoerythrin at 2.2 ångströms
1EYX: “Crystal structure of R-phycoerythrin at 2.2 ångströms”. X-ray diffraction, 4 ligands (CYC, PUB, BLA), 17 pockets (best druggability 0.68). MolNFT v1 #5987 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1EYX
- Type
- protein
- Length
- 693 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- R-phycoerythrin
- UniProt
- Q7SIG0, Q7SIF9
- Ligands
- CYC, PUB, BLA, SO4
- Pockets
- 17 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, K | R-phycoerythrin | protein | 164 | 76% helix, 0% strand | Q7SIG0 |
| B, L | R-phycoerythrin | protein | 177 | 71% helix, 0% strand | Q7SIF9 |
| G | R-phycoerythrin | protein | 6 | 67% helix, 0% strand | — |
| H | R-phycoerythrin | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 7 copies · chains A, B, G, K, L, H
- PUB · Phycourobilin · ligand · 2 copies · chains B, L
- BLA · Biliverdine IX alpha · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
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 | 177 | 0.68 | 0.87 | 28 | empty |
| 2 | 218 | 0.67 | 0.85 | 32 | empty |
| 3 | 250 | 0.62 | 0.81 | 35 | empty |
| 4 | 231 | 0.61 | 0.81 | 37 | empty |
| 5 | 164 | 0.61 | 0.83 | 32 | CYC |
Interfaces
7 interfaces between chains.
- A–B · 1640 Ų buried · 19 hydrogen bonds · protein-protein
- K–L · 1628 Ų buried · 20 hydrogen bonds · protein-protein
- A–K · 1009 Ų buried · 12 hydrogen bonds · protein-protein
- B–K · 337 Ų buried · 8 hydrogen bonds · protein-protein
- A–L · 330 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 4 covalent, 2 modified (phycocyanobilin attachment, covalent ligand, nonstandard, biliverdin attachment).
Compared structures
- 1EYX · Crystal structure of R-phycoerythrin at 2.2 ångströms · the same entry in another collection · chain H against H, TM-score 1.00
- Q7SIG0 · AlphaFold monomer V2.0 prediction for R-phycoerythrin alpha chain (Q7SIG0) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q7SIF9 · AlphaFold monomer V2.0 prediction for R-phycoerythrin beta chain (Q7SIF9) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q7SIG0
- Every structure of UniProt Q7SIF9
- Elsewhere: RCSB PDB 1EYX · PDBe 1EYX · UniProt Q7SIG0 · UniProt Q7SIF9
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