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Crystal structure of phycobiliprotein lyase cpct complexed with phycocyanobilin (pcb)
Analyse Crystal structure of phycobiliprotein lyase cpct complexed with phycocyanobilin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O4S
- Type
- protein
- Length
- 2,370 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phycocyanobilin lyase cpct
- EC
- 4.-.-.-
- UniProt
- Q8YLF9
- Ligands
- CYC
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | Phycocyanobilin lyase cpct (EC 4.-.-.-) | protein | 199 | 17% helix, 42% strand | Q8YLF9 |
| B, I, J, D, E, F, H, K, L | Phycocyanobilin lyase cpct (EC 4.-.-.-) | protein | 197 | 18% helix, 42% strand | Q8YLF9 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 12 copies · chains A, B, I, J, C, D, E, F, G, H, 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 | 438 | 0.84 | 0.91 | 53 | CYC |
| 2 | 380 | 0.80 | 0.89 | 35 | CYC |
| 3 | 377 | 0.80 | 0.88 | 38 | CYC |
| 4 | 348 | 0.79 | 0.88 | 38 | CYC |
| 5 | 414 | 0.79 | 0.87 | 38 | CYC |
Interfaces
20 interfaces between chains.
- A–B · 1017 Ų buried · 4 hydrogen bonds · protein-protein
- I–J · 1013 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 1010 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 1009 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 1003 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 modified, 12 disulfide (engineered, disulfide).
Compared structures
- 4O4S · Crystal structure of phycobiliprotein lyase CpcT complexed with phycocyanobilin (PCB) · the same entry in another collection · chain L against L, 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 Q8YLF9
- Elsewhere: RCSB PDB 4O4S · PDBe 4O4S · UniProt Q8YLF9
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