Research workbench
Crystal structure of the bilin-binding domain of phycobilisome core- membrane linker apce
Analyse Crystal structure of the bilin-binding domain of phycobilisome core- membrane… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XXI
- Type
- protein
- Length
- 293 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phycobiliprotein apce
- UniProt
- P80559
- Ligands
- CYC
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 83% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phycobiliprotein apce | protein | 147 | 82% helix, 0% strand | P80559 |
| B | Phycobiliprotein apce | protein | 146 | 84% helix, 0% strand | P80559 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.58 | 0.83 | 27 | CYC |
| 2 | 89 | 0.53 | 0.84 | 19 | CYC |
| 3 | 65 | 0.41 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1493 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (phycocyanobilin attachment).
Compared structures
- 4XXI · Crystal structure of the Bilin-binding domain of phycobilisome core-membrane linker ApcE · the same entry in another collection · chain A against A, TM-score 1.00
- P80559 · AlphaFold monomer V2.0 prediction for phycobiliprotein apce (P80559) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P80559
- Elsewhere: RCSB PDB 4XXI · PDBe 4XXI · UniProt P80559
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