MolNFT v1 · #71615 · protein
Crystal structure of human RAB5A in complex with the C2H2 zinc finger of EEA1
3MJH · RAS-related protein rab-5A: “Crystal structure of human RAB5A in complex with the C2H2 zinc finger of EEA1”. X-ray diffraction, 3 ligands (GTP, MG, ZN), 3 pockets (best druggability 0.75). MolNFT v1 #71615 on GenesisL1: 3D…
- 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
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