MolNFT v1 · #61423 · protein
Hexagonal structure of the ldh domain of human ubiquitin- conjugating enzyme E2-like isoform a
3DL2 · Ubiquitin-conjugating enzyme E2 variant 3: “Hexagonal structure of the ldh domain of human ubiquitin- conjugating enzyme E2-like isoform a”. X-ray diffraction, 2 ligands (NA, PO4), 10 pockets (best druggability 0.64). MolNFT v1…
- PDB
- 3DL2
- Type
- protein
- Length
- 576 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 variant 3
- UniProt
- Q8IX04
- Ligands
- NA, PO4
- Pockets
- 10 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme E2 variant 3 | protein | 289 | 43% helix, 20% strand | Q8IX04 |
| B | Ubiquitin-conjugating enzyme E2 variant 3 | protein | 287 | 44% helix, 20% strand | Q8IX04 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.64 | 0.95 | 13 | empty |
| 2 | 172 | 0.45 | 0.75 | 21 | empty |
| 3 | 146 | 0.42 | 0.75 | 27 | empty |
| 4 | 100 | 0.42 | 0.77 | 28 | empty |
| 5 | 67 | 0.37 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2056 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3DL2 · Hexagonal structure of the LDH domain of Human Ubiquitin-conjugating Enzyme E2-like… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8IX04 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 variant 3 (Q8IX04) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q8IX04
- Elsewhere: RCSB PDB 3DL2 · PDBe 3DL2 · UniProt Q8IX04
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