Research workbench
Crystal structure of the human COPB2 wd-domain in complex with oicr- 6254
Analyse Crystal structure of the human COPB2 wd-domain in complex with oicr- 6254 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8D41
- Type
- protein
- Length
- 606 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coatomer subunit beta'
- UniProt
- P35606
- Ligands
- Q93, UNX
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coatomer subunit beta' | protein | 307 | 1% helix, 55% strand | P35606 |
| B | Coatomer subunit beta' | protein | 299 | 1% helix, 57% strand | P35606 |
Ligands and binding sites
- Q93 · (1R,2R,3S,4S)-3-[4-(4-fluorophenyl)piperazine-1-carbonyl]bicyclo[2.2.1]heptane-2-carboxylic acid · ligand · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · chains A
- GOL · Glycerol · additive · chains A
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 | 1008 | 0.81 | 0.82 | 83 | Q93 |
| 2 | 722 | 0.79 | 0.83 | 56 | empty |
| 3 | 120 | 0.38 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 319 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 8D41 · Crystal structure of the human COPB2 WD-domain in complex with OICR-6254 · the same entry in another collection · chain A against A, TM-score 1.00
- P35606 · AlphaFold monomer V2.0 prediction for coatomer subunit beta' (P35606) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P35606
- Elsewhere: RCSB PDB 8D41 · PDBe 8D41 · UniProt P35606
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