Research workbench
Structure of an E2-E3 complex
Analyse Structure of an E2-E3 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CCG
- Type
- protein
- Length
- 446 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 T; E3 ubiquitin-protein ligase fancl
- EC
- 6.3.2.-
- UniProt
- Q9NPD8, Q9NW38
- Ligands
- ZN, NA, SO4, CL, NH4
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme E2 T | protein | 157 | 36% helix, 17% strand | Q9NPD8 |
| B | Ubiquitin-conjugating enzyme E2 T | protein | 147 | 38% helix, 17% strand | Q9NPD8 |
| X | E3 ubiquitin-protein ligase fancl (EC 6.3.2.-) | protein | 75 | 11% helix, 25% strand | Q9NW38 |
| Y | E3 ubiquitin-protein ligase fancl (EC 6.3.2.-) | protein | 67 | 12% helix, 24% strand | Q9NW38 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains X, Y
- NA · Sodium ion · metal · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains A, X, Y
- CL · Chloride ion · ion · chains B, X, Y
- NH4 · Ammonium ion · ion · chains X
- GOL · Glycerol · additive · 4 copies · chains A, B, X
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, X
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 | 620 | 0.75 | 0.81 | 62 | CL, GOL |
| 2 | 109 | 0.38 | 0.75 | 19 | empty |
| 3 | 79 | 0.35 | 0.75 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–X · 803 Ų buried · 8 hydrogen bonds · protein-protein
- B–Y · 704 Ų buried · 10 hydrogen bonds · protein-protein
- B–X · 470 Ų buried · 4 hydrogen bonds · protein-protein
- X–Y · 425 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 222 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4CCG · Structure of an E2-E3 complex · the same entry in another collection · chain Y against Y, TM-score 1.00
- Q9NPD8 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 T (Q9NPD8) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q9NW38 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase fancl (Q9NW38) · a predicted model of the same protein · chain Y against A, TM-score 0.95
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 Q9NPD8
- Every structure of UniProt Q9NW38
- Elsewhere: RCSB PDB 4CCG · PDBe 4CCG · UniProt Q9NPD8 · UniProt Q9NW38
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