MolNFT v1 · #62988 · protein
Crystal structure of the human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1). northeast structural genomics consortium target HR41
3EVX · UFM1-conjugating enzyme 1: “Crystal structure of the human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1). northeast…”. X-ray diffraction, 1 ligand (SCN), 10 pockets (best druggability 0.81). MolNFT v1 #62988 on…
- PDB
- 3EVX
- Type
- protein
- Length
- 632 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UFM1-conjugating enzyme 1
- UniProt
- Q9Y3C8
- Ligands
- SCN
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | UFM1-conjugating enzyme 1 | protein | 158 | 41% helix, 18% strand | Q9Y3C8 |
Ligands and binding sites
- SCN · Thiocyanate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.81 | 0.82 | 114 | SCN |
| 2 | 83 | 0.58 | 0.87 | 22 | empty |
| 3 | 205 | 0.57 | 0.79 | 34 | empty |
| 4 | 112 | 0.39 | 0.75 | 21 | empty |
| 5 | 82 | 0.35 | 0.75 | 18 | empty |
Interfaces
5 interfaces between chains.
- B–C · 554 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 515 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 511 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 423 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 270 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3EVX · Crystal structure of the human E2-like ubiquitin-fold modifier conjugating enzyme 1… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y3C8 · AlphaFold monomer V2.0 prediction for ubiquitin-fold modifier- conjugating enzyme 1… · 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 Q9Y3C8
- Elsewhere: RCSB PDB 3EVX · PDBe 3EVX · UniProt Q9Y3C8
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