MolNFT v1 · #122510 · protein
P190A gap domain complex with rhoa
5IRC · Rho GTPase-activating protein 35: “P190A gap domain complex with rhoa”. X-ray diffraction, 4 ligands (GDP, MGF, MG), 6 pockets (best druggability 0.72). MolNFT v1 #122510 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5IRC
- Type
- protein
- Length
- 738 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rho GTPase-activating protein 35; Transforming protein rhoa
- UniProt
- P81128, P61586
- Ligands
- GDP, MGF, MG, CL
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rho GTPase-activating protein 35 | protein | 201 | 62% helix, 0% strand | P81128 |
| F | Transforming protein rhoa | protein | 170 | 39% helix, 26% strand | P61586 |
| B | Rho GTPase-activating protein 35 | protein | 196 | 63% helix, 0% strand | P81128 |
| D | Transforming protein rhoa | protein | 171 | 40% helix, 26% strand | P61586 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, F, B, D
- MGF · Trifluoromagnesate · ligand · 2 copies · chains A, F, B, D
- MG · Magnesium ion · metal · 2 copies · chains A, F, B, D
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.72 | 0.76 | 77 | CL |
| 2 | 467 | 0.68 | 0.79 | 51 | GDP, MG, MGF |
| 3 | 453 | 0.67 | 0.79 | 56 | GDP, MG, MGF |
| 4 | 384 | 0.60 | 0.77 | 46 | empty |
| 5 | 57 | 0.31 | 0.76 | 11 | empty |
Interfaces
5 interfaces between chains.
- A–F · 1299 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1250 Ų buried · 13 hydrogen bonds · protein-protein
- F–B · 332 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 185 Ų buried · 2 hydrogen bonds · protein-protein
- F–D · 69 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 5IRC · p190A GAP domain complex with RhoA · the same entry in another collection · chain D against D, TM-score 1.00
- P61586 · AlphaFold monomer V2.0 prediction for transforming protein rhoa (P61586) · a predicted model of the same protein · chain F against A, TM-score 0.99
- P81128 · AlphaFold monomer V2.0 prediction for rho GTPase-activating protein 35 (P81128) · a predicted model of the same protein · chain B 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 P81128
- Every structure of UniProt P61586
- Elsewhere: RCSB PDB 5IRC · PDBe 5IRC · UniProt P81128 · UniProt P61586
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