MolNFT v1 · #137039 · protein
Crystal structure of small molecule disulfide 2C07 bound to H-RAS M72C gppnhp
5VBZ · GTPase HRAS: “Crystal structure of small molecule disulfide 2C07 bound to H-RAS M72C gppnhp”. X-ray diffraction, 3 ligands (GNP, 92V, MG), 10 pockets (best druggability 0.77). MolNFT v1 #137039 on GenesisL1: 3D structure, binding…
- PDB
- 5VBZ
- Type
- protein
- Length
- 483 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase HRAS
- UniProt
- P01112
- Ligands
- GNP, 92V, MG
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase HRAS | protein | 155 | 34% helix, 29% strand | P01112 |
| B, C | GTPase HRAS | protein | 164 | 38% helix, 26% strand | P01112 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 3 copies · chains A, B, C
- 92V · 1-(4-methoxyphenyl)-N-(3-sulfanylpropyl)-5-(trifluoromethyl)-1H-pyrazole-4-carboxamide · ligand · chains C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.77 | 0.81 | 72 | empty |
| 2 | 153 | 0.50 | 0.79 | 29 | GNP, MG |
| 3 | 153 | 0.47 | 0.77 | 29 | empty |
| 4 | 117 | 0.46 | 0.78 | 17 | 92V |
| 5 | 97 | 0.44 | 0.79 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 952 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 345 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 237 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5VBZ · Crystal Structure of Small Molecule Disulfide 2C07 Bound to H-Ras M72C GppNHp · the same entry in another collection · chain A against A, TM-score 1.00
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 P01112
- Elsewhere: RCSB PDB 5VBZ · PDBe 5VBZ · UniProt P01112
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