MolNFT v1 · #77442 · protein
Shigella ipaa-VBS3 in complex with human vinculin
3RF3: “Shigella ipaa-VBS3 in complex with human vinculin”. X-ray diffraction, 6 pockets (best druggability 0.74). MolNFT v1 #77442 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3RF3
- Type
- protein
- Length
- 562 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vinculin; Invasin ipaa
- UniProt
- P18206, P18010
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 79% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vinculin | protein | 257 | 80% helix, 1% strand | P18206 |
| B | Vinculin | protein | 258 | 79% helix, 1% strand | P18206 |
| C | Invasin ipaa | protein | 23 | 70% helix, 0% strand | P18010 |
| D | Invasin ipaa | protein | 24 | 67% helix, 0% strand | P18010 |
Ligands and binding sites
- CAC · Cacodylate ion · additive · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 847 | 0.74 | 0.78 | 68 | empty |
| 2 | 254 | 0.58 | 0.78 | 34 | CAC |
| 3 | 234 | 0.56 | 0.78 | 30 | empty |
| 4 | 241 | 0.49 | 0.75 | 32 | empty |
| 5 | 73 | 0.36 | 0.77 | 22 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1193 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1157 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 348 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 341 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 200 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3RF3 · Shigella IpaA-VBS3 in complex with human vinculin · the same entry in another collection · chain D against D, TM-score 1.00
- P18206 · AlphaFold monomer V2.0 prediction for vinculin (P18206) · a predicted model of the same protein · chain A against A, TM-score 0.90
- P18010 · AlphaFold monomer V2.0 prediction for invasin ipaa (P18010) · a predicted model of the same protein · chain C against A, TM-score 0.74
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 P18206
- Every structure of UniProt P18010
- Elsewhere: RCSB PDB 3RF3 · PDBe 3RF3 · UniProt P18206 · UniProt P18010
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