MolNFT v1 · #39966 · protein
Human VINCULIN'S head domain (VH1, residues 1-258) in complex with two vinculin binding sites of shigella FLEXNERI'S ipaa (residues 565-587)
2IBF: “Human VINCULIN'S head domain (VH1, residues 1-258) in complex with two vinculin binding sites of shigella…”. X-ray diffraction, 3 pockets (best druggability 0.41). MolNFT v1 #39966 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2IBF
- Type
- protein
- Length
- 302 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vinculin; Invasin ipaa
- UniProt
- P18206, P18010
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 3 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vinculin | protein | 258 | 80% helix, 0% strand | P18206 |
| B | Invasin ipaa | protein | 25 | 68% helix, 0% strand | P18010 |
| D | Invasin ipaa | protein | 19 | 84% helix, 0% strand | P18010 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.41 | 0.80 | 17 | empty |
| 2 | 79 | 0.36 | 0.76 | 12 | empty |
| 3 | 58 | 0.34 | 0.78 | 13 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1314 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 661 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2IBF · Human vinculin's head domain (Vh1, residues 1-258) in complex with two vinculin binding… · the same entry in another collection · chain A against A, 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 0.83
- P18010 · AlphaFold monomer V2.0 prediction for invasin ipaa (P18010) · a predicted model of the same protein · chain D against A, TM-score 0.75
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 2IBF · PDBe 2IBF · UniProt P18206 · UniProt P18010
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