MolNFT v1 · #93809 · protein
Crystal structure of the binary complex of KRIT1 bound to the RAP1 GTPase
4HDO · Krev interaction trapped protein 1: “Crystal structure of the binary complex of KRIT1 bound to the RAP1 GTPase”. X-ray diffraction, 2 ligands (GNP, MG), 10 pockets (best druggability 0.68). MolNFT v1 #93809 on GenesisL1: 3D…
- 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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