Research workbench
Crystal structure of the RLIP76 ral binding domain mutant (E427S/L429M/Q433L/K440R) in complex with ralb-gmppnp
Analyse Crystal structure of the RLIP76 ral binding domain mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZRN
- Type
- protein
- Length
- 454 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein ral-B; Rala-binding protein 1
- UniProt
- P11234, Q15311
- Ligands
- GNP, MG
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RAS-related protein ral-B | protein | 173 | 42% helix, 27% strand | P11234 |
| C | Rala-binding protein 1 | protein | 51 | 82% helix, 0% strand | Q15311 |
| 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 · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.77 | 0.79 | 84 | GNP, MG, GOL |
| 2 | 384 | 0.66 | 0.80 | 39 | GNP, MG, GOL |
| 3 | 131 | 0.43 | 0.76 | 19 | empty |
| 4 | 113 | 0.41 | 0.76 | 21 | empty |
| 5 | 108 | 0.39 | 0.75 | 17 | empty |
Interfaces
4 interfaces between chains.
- B–C · 938 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 887 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 285 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 39 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ZRN · Crystal structure of the RLIP76 Ral binding domain mutant (E427S/L429M/Q433L/K440R) in… · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.98
- 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 6ZRN · PDBe 6ZRN · UniProt P11234 · UniProt Q15311
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