MolNFT v1 · #54427 · protein
C-terminal cysteine-rich domain of human chfr bound to madpr
2XOC · E3 ubiquitin-protein ligase chfr: “C-terminal cysteine-rich domain of human chfr bound to madpr”. X-ray diffraction, 3 ligands (ADE, ADP, ZN), 3 pockets (best druggability 0.58). MolNFT v1 #54427 on GenesisL1: 3D structure, binding…
- PDB
- 2XOC
- Type
- protein
- Length
- 425 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
- ADE, ADP, ZN
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase chfr (EC 6.3.2.-) | protein | 213 | 36% helix, 8% strand | Q96EP1 |
| B | E3 ubiquitin-protein ligase chfr (EC 6.3.2.-) | protein | 212 | 38% helix, 8% strand | Q96EP1 |
Ligands and binding sites
- ADE · Adenine · ligand · 2 copies · chains B
- ADP · Adenosine-5'-diphosphate · ligand · chains A, B
- ZN · Zinc ion · metal · 10 copies · chains A, B
- PGE · Triethylene glycol · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.58 | 0.81 | 26 | ADP |
| 2 | 57 | 0.28 | 0.74 | 16 | empty |
| 3 | 57 | 0.27 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 473 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2XOC · C-terminal cysteine-rich domain of human CHFR bound to mADPr · 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 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 Q96EP1
- Elsewhere: RCSB PDB 2XOC · PDBe 2XOC · UniProt Q96EP1
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