Research workbench
C-terminal cysteine-rich domain of human chfr bound to P(1), P(2)-diadenosine-5'-pyrophosphate
Analyse C-terminal cysteine-rich domain of human chfr bound to P(1)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XOY
- Type
- protein
- Length
- 426 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase chfr
- EC
- 6.3.2.-
- UniProt
- Q96EP1
- Ligands
- AMP, ADE, ZN
- Pockets
- 1 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase chfr (EC 6.3.2.-) | protein | 212 | 39% helix, 8% strand | Q96EP1 |
| B | E3 ubiquitin-protein ligase chfr (EC 6.3.2.-) | protein | 214 | 36% helix, 7% strand | Q96EP1 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains B
- ADE · Adenine · ligand · chains B
- ZN · Zinc ion · metal · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.60 | 0.81 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 449 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2XOY · C-terminal cysteine-rich domain of human CHFR bound to P(1),P(2)… · the same entry in another collection · chain A against A, TM-score 1.00
- Q96EP1 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase chfr (Q96EP1) · 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 Q96EP1
- Elsewhere: RCSB PDB 2XOY · PDBe 2XOY · UniProt Q96EP1
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