MolNFT v2 · #173999 · protein
Crystal structure of the RLIP76 Ral binding domain mutant (E427H/Q433L/K440R) in complex with RalB-GMPPNP
6ZQT · Ras-related protein Ral-B: “Crystal structure of the RLIP76 Ral binding domain mutant (E427H/Q433L/K440R) in complex with RalB-GMPPNP”. X-ray diffraction at 1.51, 2 ligands (GNP, MG), 6 pockets (best druggability 0.77). MolNFT v2…
- PDB
- 6ZQT
- Type
- protein
- Length
- 452 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.51
- Source
- Homo sapiens
- Molecule
- Ras-related protein Ral-B; RalA-binding protein 1
- UniProt
- P11234, Q15311
- Ligands
- GNP, MG
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.51 · 4 distinct chains · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ras-related protein Ral-B | protein | 173 | 41% helix, 26% strand | P11234 |
| C | RalA-binding protein 1 | protein | 51 | 82% helix, 0% strand | Q15311 |
| B | Ras-related protein Ral-B | protein | 171 | 41% helix, 26% strand | P11234 |
| D | RalA-binding protein 1 | protein | 57 | 75% helix, 0% strand | Q15311 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.77 | 0.79 | 86 | GNP, MG, GOL |
| 2 | 399 | 0.66 | 0.80 | 40 | GNP, MG |
| 3 | 137 | 0.44 | 0.76 | 18 | empty |
| 4 | 83 | 0.44 | 0.80 | 18 | empty |
| 5 | 77 | 0.40 | 0.78 | 19 | empty |
Interfaces
4 interfaces between chains.
- B–D · 925 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 903 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 277 Ų buried · 2 hydrogen bonds · protein-protein
- C–B · 62 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6ZQT · Crystal structure of the RLIP76 ral binding domain mutant (E427H/Q433L/K440R) in complex… · the same entry in another collection · chain D against D, TM-score 1.00
- P11234 · AlphaFold monomer V2.0 prediction for RAS-related protein ral-B (P11234) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q15311 · AlphaFold monomer V2.0 prediction for rala-binding protein 1 (Q15311) · a predicted model of the same protein · chain C against A, TM-score 0.89
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 P11234
- Every structure of UniProt Q15311
- Elsewhere: RCSB PDB 6ZQT · PDBe 6ZQT · UniProt P11234 · UniProt Q15311
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