Research workbench
Crystal structure of rabex-5DELTA and rabaptin-5C21 complex
Analyse Crystal structure of rabex-5DELTA and rabaptin-5C21 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N3Z
- Type
- protein
- Length
- 403 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAB5 GDP/GTP exchange factor; Rab GTPase-binding effector protein 1
- UniProt
- Q9UJ41, Q15276
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAB5 GDP/GTP exchange factor | protein | 238 | 72% helix, 0% strand | Q9UJ41 |
| B | Rab GTPase-binding effector protein 1 | protein | 82 | 84% helix, 0% strand | Q15276 |
| C | Rab GTPase-binding effector protein 1 | protein | 83 | 88% helix, 0% strand | Q15276 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
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 | 650 | 0.71 | 0.78 | 79 | empty |
| 2 | 159 | 0.47 | 0.76 | 21 | empty |
| 3 | 59 | 0.32 | 0.76 | 13 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1959 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1088 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 733 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4N3Z · Crystal structure of Rabex-5delta and Rabaptin-5C21 complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UJ41 · AlphaFold monomer V2.0 prediction for RAB5 GDP/GTP exchange factor (Q9UJ41) · a predicted model of the same protein · chain A against A, TM-score 0.81
- Q15276 · AlphaFold monomer V2.0 prediction for rab GTPase-binding effector protein 1 (Q15276) · a predicted model of the same protein · chain B against A, TM-score 0.65
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 Q9UJ41
- Every structure of UniProt Q15276
- Elsewhere: RCSB PDB 4N3Z · PDBe 4N3Z · UniProt Q9UJ41 · UniProt Q15276
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