Research workbench
Monobody 12VC3 bound to HRAS(WT)
Analyse Monobody 12VC3 bound to HRAS(WT) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L0F
- Type
- protein
- Length
- 1,037 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase HRAS; Monobody 12VC3
- EC
- 3.6.5.2
- UniProt
- P01112
- Ligands
- GSP, MG
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, A, G, L | GTPase HRAS (EC 3.6.5.2) | protein | 166 | 37% helix, 27% strand | P01112 |
| F, B, M | Monobody 12VC3 | protein | 93 | 0% helix, 59% strand | — |
| H | Monobody 12VC3 | protein | 94 | 0% helix, 59% strand | — |
Ligands and binding sites
- GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 4 copies · chains E, F, A, B, G, H, L, M
- MG · Magnesium ion · metal · 4 copies · chains E, A, G, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1197 | 0.86 | 0.87 | 120 | MG, GSP |
| 2 | 314 | 0.76 | 0.88 | 48 | MG, GSP |
| 3 | 477 | 0.73 | 0.82 | 43 | empty |
| 4 | 541 | 0.73 | 0.81 | 57 | empty |
| 5 | 274 | 0.69 | 0.84 | 45 | MG, GSP |
Interfaces
10 interfaces between chains.
- A–B · 911 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 904 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 897 Ų buried · 14 hydrogen bonds · protein-protein
- L–M · 887 Ų buried · 13 hydrogen bonds · protein-protein
- A–G · 676 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7L0F · Monobody 12VC3 Bound to HRAS(WT) · the same entry in another collection · chain E against E, 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 7L0F · PDBe 7L0F · UniProt P01112
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