Research workbench
2.05 a resolution structure of ipad from shigella flexneri in complex with single-domain antibody 20IPAD
Analyse 2.05 a resolution structure of ipad from shigella flexneri in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VXM
- Type
- protein
- Length
- 368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Invasin ipad; Single-domain antibody 20IPAD
- UniProt
- P18013
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Invasin ipad | protein | 243 | 70% helix, 9% strand | P18013 |
| B | Single-domain antibody 20IPAD | protein | 125 | 7% helix, 47% strand | — |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.45 | 0.78 | 23 | empty |
| 2 | 53 | 0.39 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 648 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5VXM · 2.05 A resolution structure of IpaD from Shigella flexneri in complex with single-domain… · the same entry in another collection · chain A against A, TM-score 1.00
- P18013 · AlphaFold monomer V2.0 prediction for invasin ipad (P18013) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P18013
- Elsewhere: RCSB PDB 5VXM · PDBe 5VXM · UniProt P18013
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