MolNFT v1 · #93811 · protein
Crystal structure of the ternary complex of KRIT1 bound to both the RAP1 GTPase and the heart of glass (HEG1) cytoplasmic tail
4HDQ · Krev interaction trapped protein 1: “Crystal structure of the ternary complex of KRIT1 bound to both the RAP1 GTPase and the heart of glass (HEG1)…”. X-ray diffraction, 2 ligands (GNP, MG), 8 pockets (best druggability 0.75). MolNFT…
- PDB
- 4HDQ
- Type
- protein
- Length
- 480 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 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
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