Research workbench
Crystal structure of UBCH5B in complex with the ring-U5BR fragment of AO7 (P199A)
Analyse Crystal structure of UBCH5B in complex with the ring-U5BR fragment of AO7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D1M
- Type
- protein
- Length
- 256 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 D2; E3 ubiquitin-protein ligase RNF25
- EC
- 6.3.2.19, 6.3.2.-
- UniProt
- P62837, Q96BH1
- Ligands
- OXL, ZN
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme E2 D2 (EC 6.3.2.19) | protein | 146 | 36% helix, 21% strand | P62837 |
| B | E3 ubiquitin-protein ligase RNF25 (EC 6.3.2.-) | protein | 110 | 39% helix, 10% strand | Q96BH1 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
- PEG · Di(hydroxyethyl)ether · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 205 | 0.55 | 0.78 | 32 | empty |
| 2 | 98 | 0.52 | 0.83 | 16 | empty |
| 3 | 66 | 0.39 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1624 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5D1M · Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (P199A) · the same entry in another collection · chain A against A, TM-score 1.00
- P62837 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D2 (P62837) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q96BH1 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF25 (Q96BH1) · a predicted model of the same protein · chain B against A, TM-score 0.85
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 P62837
- Every structure of UniProt Q96BH1
- Elsewhere: RCSB PDB 5D1M · PDBe 5D1M · UniProt P62837 · UniProt Q96BH1
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