Research workbench
Crystal structure of APC/C hetero-tetramer CUT9-HCN1
Analyse Crystal structure of APC/C hetero-tetramer CUT9-HCN1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XPI
- Type
- protein
- Length
- 1,084 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anaphase-promoting complex subunit CUT9; Anaphase-promoting complex subunit HCN1…
- UniProt
- P41889, O13916
- Ligands
- ACE, AUC
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anaphase-promoting complex subunit CUT9 | protein | 520 | 76% helix, 0% strand | P41889 |
| B, E | Anaphase-promoting complex subunit HCN1 HCN1/CDC26,20S CYCLOSOME/APC complex protein HCN1, chaperone-like protein HCN1, high copy suppressor of CUT9 protein 1 | protein | 23 | 35% helix, 0% strand | O13916 |
| D | Anaphase-promoting complex subunit CUT9 | protein | 518 | 74% helix, 0% strand | P41889 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, B, D, E
- AUC · Gold (I) cyanide ion · metal · 4 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.84 | 0.85 | 85 | ACE, AUC |
| 2 | 1011 | 0.83 | 0.84 | 74 | AUC |
| 3 | 272 | 0.59 | 0.79 | 45 | empty |
| 4 | 228 | 0.56 | 0.78 | 32 | empty |
| 5 | 50 | 0.40 | 0.81 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–D · 3159 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 1486 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1472 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2XPI · Crystal structure of APC/C hetero-tetramer Cut9-Hcn1 · the same entry in another collection · chain A against A, TM-score 1.00
- P41889 · AlphaFold monomer V2.0 prediction for anaphase-promoting complex subunit CUT9 (P41889) · a predicted model of the same protein · chain A against A, TM-score 1.00
- O13916 · AlphaFold monomer V2.0 prediction for anaphase-promoting complex subunit HCN1 (O13916) · a predicted model of the same protein · chain B against A, TM-score 0.48
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 P41889
- Every structure of UniProt O13916
- Elsewhere: RCSB PDB 2XPI · PDBe 2XPI · UniProt P41889 · UniProt O13916
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