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Crystal structure of orange carotenoid protein with partial loss of 3'OH echinenone chromophore
Analyse Crystal structure of orange carotenoid protein with partial loss of 3'OH… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TUW
- Type
- protein
- Length
- 1,830 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orange carotenoid-binding protein
- UniProt
- P74102
- Ligands
- EQ3
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F | Orange carotenoid-binding protein | protein | 305 | 47% helix, 18% strand | P74102 |
| B | Orange carotenoid-binding protein | protein | 304 | 47% helix, 18% strand | P74102 |
| D | Orange carotenoid-binding protein | protein | 306 | 47% helix, 17% strand | P74102 |
Ligands and binding sites
- EQ3 · (3'R)-3'-hydroxy-beta,beta-caroten-4-one · ligand · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 4 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.87 | 0.92 | 61 | EQ3 |
| 2 | 567 | 0.87 | 0.92 | 61 | EQ3 |
| 3 | 560 | 0.87 | 0.92 | 58 | EQ3 |
| 4 | 609 | 0.86 | 0.91 | 70 | GOL, EQ3 |
| 5 | 693 | 0.86 | 0.89 | 76 | EQ3 |
Interfaces
9 interfaces between chains.
- C–D · 1189 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1174 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1171 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 607 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 601 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5TUW · Crystal structure of Orange Carotenoid Protein with partial loss of 3'OH Echine… · the same entry in another collection · chain F against F, TM-score 1.00
- P74102 · AlphaFold monomer V2.0 prediction for orange carotenoid-binding protein (P74102) · a predicted model of the same protein · chain B 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 P74102
- Elsewhere: RCSB PDB 5TUW · PDBe 5TUW · UniProt P74102
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