Research workbench
Crystal structure of a bovine rabex-5 fragment complexed with ubiquitin
Analyse Crystal structure of a bovine rabex-5 fragment complexed with ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FIF
- Type
- protein
- Length
- 392 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; RAB5 GDP/GTP exchange factor
- UniProt
- P62990, O18973
- Ligands
- ZN, SO4
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Ubiquitin | protein | 73 | 26% helix, 36% strand | P62990 |
| B | RAB5 GDP/GTP exchange factor | protein | 59 | 64% helix, 7% strand | O18973 |
| D | RAB5 GDP/GTP exchange factor | protein | 58 | 64% helix, 7% strand | O18973 |
| F | RAB5 GDP/GTP exchange factor | protein | 56 | 61% helix, 0% strand | O18973 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.57 | 0.78 | 26 | empty |
| 2 | 212 | 0.50 | 0.76 | 26 | empty |
| 3 | 190 | 0.48 | 0.76 | 26 | empty |
| 4 | 72 | 0.32 | 0.75 | 16 | empty |
| 5 | 54 | 0.25 | 0.73 | 10 | empty |
Interfaces
8 interfaces between chains.
- C–D · 765 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 757 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 745 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 438 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 155 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2FIF · Crystal Structure of a Bovine Rabex-5 fragment complexed with ubiquitin · the same entry in another collection · chain F against F, TM-score 1.00
- O18973 · AlphaFold monomer V2.0 prediction for RAB5 GDP/GTP exchange factor (O18973) · a predicted model of the same protein · chain B against A, TM-score 0.84
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 P62990
- Every structure of UniProt O18973
- Elsewhere: RCSB PDB 2FIF · PDBe 2FIF · UniProt P62990 · UniProt O18973
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