Research workbench
Crystal structure of the binary complex of KRIT1 bound to the RAP1 GTPase
Analyse Crystal structure of the binary complex of KRIT1 bound to 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
- 4HDO
- Type
- protein
- Length
- 473 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Krev interaction trapped protein 1; RAS-related protein rap-1B
- UniProt
- O00522, P61224
- Ligands
- GNP, MG
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Krev interaction trapped protein 1 | protein | 310 | 39% helix, 23% strand | O00522 |
| B | RAS-related protein rap-1B | protein | 163 | 37% helix, 29% strand | P61224 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains 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
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 525 | 0.68 | 0.78 | 49 | empty |
| 2 | 174 | 0.64 | 0.85 | 29 | empty |
| 3 | 199 | 0.62 | 0.83 | 32 | GOL |
| 4 | 149 | 0.58 | 0.83 | 29 | MG, GNP |
| 5 | 167 | 0.58 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 832 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4HDO · Crystal structure of the binary Complex of KRIT1 bound to the Rap1 GTPase · 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
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
- Elsewhere: RCSB PDB 4HDO · PDBe 4HDO · UniProt O00522 · UniProt P61224
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