Research workbench
Structure of the CIAP2 ring domain bound to UBCH5B
Analyse Structure of the CIAP2 ring domain bound to UBCH5B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EB6
- Type
- protein
- Length
- 213 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Baculoviral iap repeat-containing protein 3; Ubiquitin-conjugating enzyme E2 D2
- EC
- 6.3.2.19
- UniProt
- Q13489, P62840
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Baculoviral iap repeat-containing protein 3 | protein | 64 | 16% helix, 23% strand | Q13489 |
| B | Ubiquitin-conjugating enzyme E2 D2 (EC 6.3.2.19) | protein | 149 | 35% helix, 17% strand | P62840 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 192 | 0.49 | 0.77 | 22 | empty |
| 2 | 78 | 0.34 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 620 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3EB6 · Structure of the cIAP2 RING domain bound to UbcH5b · the same entry in another collection · chain A against A, TM-score 1.00
- P62840 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D2 (P62840) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q13489 · AlphaFold monomer V2.0 prediction for baculoviral iap repeat- containing protein 3… · a predicted model of the same protein · chain A against A, TM-score 0.79
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 Q13489
- Every structure of UniProt P62840
- Elsewhere: RCSB PDB 3EB6 · PDBe 3EB6 · UniProt Q13489 · UniProt P62840
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