MolNFT v1 · #70843 · protein
Shigella IPGB2 in complex with human rhoa, GDP and MG2+ (complex B)
3LWN · Transforming protein rhoa: “Shigella IPGB2 in complex with human rhoa, GDP and MG2+ (complex B)”. X-ray diffraction, 2 ligands (GDP, MG), 10 pockets (best druggability 0.71). MolNFT v1 #70843 on GenesisL1: 3D structure, binding…
- PDB
- 3LWN
- Type
- protein
- Length
- 724 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transforming protein rhoa; IPGB2
- UniProt
- P61586, Q9AJW7
- Ligands
- GDP, MG
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Transforming protein rhoa | protein | 181 | 38% helix, 23% strand | P61586 |
| F, G | IPGB2 | protein | 181 | 61% helix, 13% strand | Q9AJW7 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.71 | 0.86 | 37 | empty |
| 2 | 227 | 0.70 | 0.86 | 33 | empty |
| 3 | 306 | 0.58 | 0.77 | 34 | GDP, MG |
| 4 | 306 | 0.57 | 0.77 | 33 | GDP, MG |
| 5 | 313 | 0.54 | 0.75 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–F · 1453 Ų buried · 29 hydrogen bonds · protein-protein
- B–G · 1422 Ų buried · 28 hydrogen bonds · protein-protein
- B–F · 117 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3LWN · Shigella IpgB2 in complex with human RhoA, GDP and Mg2+ (complex B) · 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 A against A, TM-score 0.95
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 3LWN · PDBe 3LWN · UniProt P61586 · UniProt Q9AJW7
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