MolNFT v1 · #121258 · protein
Crystal structure of RHOA.GDP.MGF3-in complex with human myosin 9B rhogap domain
5HPY · Unconventional myosin-ixb: “Crystal structure of RHOA.GDP.MGF3-in complex with human myosin 9B rhogap domain”. X-ray diffraction, 3 ligands (MGF, GDP, MG), 7 pockets (best druggability 0.72). MolNFT v1 #121258 on GenesisL1: 3D…
- PDB
- 5HPY
- Type
- protein
- Length
- 738 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unconventional myosin-ixb; Transforming protein rhoa
- UniProt
- Q13459, P61586
- Ligands
- MGF, GDP, MG
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 59% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Unconventional myosin-ixb | protein | 192 | 67% helix, 0% strand | Q13459 |
| B, F | Transforming protein rhoa | protein | 178 | 40% helix, 26% strand | P61586 |
| D | Unconventional myosin-ixb | protein | 190 | 68% helix, 0% strand | Q13459 |
Ligands and binding sites
- MGF · Trifluoromagnesate · ligand · 2 copies · chains A, B, D, F
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B, D, F
- MG · Magnesium ion · metal · 3 copies · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 596 | 0.72 | 0.80 | 74 | MGF, MG, GDP |
| 2 | 499 | 0.69 | 0.80 | 55 | MGF, GDP, MG |
| 3 | 100 | 0.57 | 0.86 | 20 | empty |
| 4 | 81 | 0.54 | 0.86 | 23 | empty |
| 5 | 94 | 0.53 | 0.85 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1221 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 1214 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 216 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5HPY · Crystal Structure of RhoA.GDP.MgF3-in complex with human Myosin 9b RhoGAP domain · the same entry in another collection · chain A against A, TM-score 1.00
- P61586 · AlphaFold monomer V2.0 prediction for transforming protein rhoa (P61586) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q13459 · AlphaFold monomer V2.0 prediction for unconventional myosin-ixb (Q13459) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 Q13459
- Every structure of UniProt P61586
- Elsewhere: RCSB PDB 5HPY · PDBe 5HPY · UniProt Q13459 · UniProt P61586
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