Research workbench
Crystal structure of human RAB5A in complex with the C2H2 zinc finger of EEA1
Analyse Crystal structure of human RAB5A in complex with the C2H2 zinc finger of EEA1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MJH
- Type
- protein
- Length
- 402 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-5A; Early endosome antigen 1
- EC
- 3.6.5.2
- UniProt
- P20339, Q15075
- Ligands
- GTP, MG, ZN
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-5A (EC 3.6.5.2) | protein | 168 | 38% helix, 29% strand | P20339 |
| B | Early endosome antigen 1 | protein | 34 | 32% helix, 18% strand | Q15075 |
| C | RAS-related protein rab-5A (EC 3.6.5.2) | protein | 167 | 37% helix, 28% strand | P20339 |
| D | Early endosome antigen 1 | protein | 33 | 33% helix, 18% strand | Q15075 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains B, D
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 | 736 | 0.75 | 0.80 | 64 | GTP, MG |
| 2 | 216 | 0.51 | 0.76 | 21 | empty |
| 3 | 140 | 0.49 | 0.79 | 25 | GTP, MG |
Interfaces
4 interfaces between chains.
- C–D · 651 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 619 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 385 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 303 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3MJH · Crystal Structure of Human Rab5A in complex with the C2H2 Zinc Finger of EEA1 · the same entry in another collection · chain D against D, TM-score 1.00
- P20339 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-5A (P20339) · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q15075 · AlphaFold monomer V2.0 prediction for early endosome antigen 1 (Q15075) · a predicted model of the same protein · chain D against A, TM-score 0.50
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 P20339
- Every structure of UniProt Q15075
- Elsewhere: RCSB PDB 3MJH · PDBe 3MJH · UniProt P20339 · UniProt Q15075
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.