Research workbench
Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and the Heart of Glass (HEG1) cytoplasmic tail
Analyse Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HDQ
- Type
- protein
- Length
- 480 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.95
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Krev interaction trapped protein 1; Ras-related protein Rap-1b; Protein HEG homolog 1
- UniProt
- O00522, P61224, Q9ULI3
- Ligands
- GNP, MG
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · resolution 1.95 · 3 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Krev interaction trapped protein 1 | protein | 311 | 39% helix, 23% strand | O00522 |
| B | Ras-related protein Rap-1b | protein | 164 | 37% helix, 27% strand | P61224 |
| C | Protein HEG homolog 1 | protein | 5 | 0% helix, 0% strand | Q9ULI3 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A, B
- MG · Magnesium ion · metal · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.75 | 0.80 | 85 | GOL |
| 2 | 163 | 0.68 | 0.87 | 26 | empty |
| 3 | 209 | 0.54 | 0.78 | 29 | MG, GNP |
| 4 | 84 | 0.42 | 0.79 | 15 | empty |
| 5 | 69 | 0.34 | 0.76 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 912 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 489 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4HDQ · Crystal structure of the ternary complex of KRIT1 bound to both the RAP1 GTPase and the… · the same entry in another collection · chain A against A, TM-score 1.00
- O00522 · AlphaFold monomer V2.0 prediction for krev interaction trapped protein 1 (O00522) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P61224 · AlphaFold monomer V2.0 prediction for RAS-related protein rap-1B (P61224) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q9ULI3 · AlphaFold monomer V2.0 prediction for protein heg homolog 1 (Q9ULI3) · a predicted model of the same protein · chain C against A, TM-score 0.64
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 O00522
- Every structure of UniProt P61224
- Every structure of UniProt Q9ULI3
- Elsewhere: RCSB PDB 4HDQ · PDBe 4HDQ · UniProt O00522 · UniProt P61224 · UniProt Q9ULI3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.