Research workbench
Shigella IPGB2 in complex with human rhoa, GDP and MG2+ (complex a)
Analyse Shigella IPGB2 in complex with human rhoa, GDP and MG2+ (complex a) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LW8
- Type
- protein
- Length
- 1,460 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transforming protein rhoa; IPGB2
- UniProt
- P61586, Q9AJW7
- Ligands
- GDP, MG
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Transforming protein rhoa | protein | 185 | 40% helix, 23% strand | P61586 |
| D | Transforming protein rhoa | protein | 181 | 38% helix, 22% strand | P61586 |
| E, F, G, H | IPGB2 | protein | 181 | 61% helix, 13% strand | Q9AJW7 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.73 | 0.83 | 58 | empty |
| 2 | 274 | 0.72 | 0.87 | 38 | empty |
| 3 | 272 | 0.71 | 0.86 | 38 | empty |
| 4 | 280 | 0.71 | 0.85 | 38 | empty |
| 5 | 765 | 0.67 | 0.75 | 67 | GDP, MG |
Interfaces
16 interfaces between chains.
- D–E · 1378 Ų buried · 25 hydrogen bonds · protein-protein
- B–G · 1352 Ų buried · 22 hydrogen bonds · protein-protein
- C–H · 1332 Ų buried · 19 hydrogen bonds · protein-protein
- A–F · 1147 Ų buried · 18 hydrogen bonds · protein-protein
- C–G · 329 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3LW8 · Shigella IpgB2 in complex with human RhoA, GDP and Mg2+ (complex A) · the same entry in another collection · chain H against H, TM-score 1.00
- P61586 · AlphaFold monomer V2.0 prediction for transforming protein rhoa (P61586) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 P61586
- Every structure of UniProt Q9AJW7
- Elsewhere: RCSB PDB 3LW8 · PDBe 3LW8 · UniProt P61586 · UniProt Q9AJW7
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