MolNFT v1 · #84065 · protein
RAS-related protein RAP1B(T65A) with gppnhp
3X1Z · RAS-related protein rap-1B: “RAS-related protein RAP1B(T65A) with gppnhp”. X-ray diffraction, 2 ligands (GNP, MG), 3 pockets (best druggability 0.69). MolNFT v1 #84065 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3X1Z
- Type
- protein
- Length
- 334 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rap-1B
- UniProt
- Q62636
- Ligands
- GNP, MG
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RAS-related protein rap-1B | protein | 167 | 37% helix, 28% strand | Q62636 |
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 · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.69 | 0.85 | 37 | GNP, MG |
| 2 | 209 | 0.68 | 0.86 | 38 | GNP, MG |
| 3 | 272 | 0.55 | 0.76 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 783 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
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 Q62636
- Elsewhere: RCSB PDB 3X1Z · PDBe 3X1Z · UniProt Q62636
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