Research workbench
2.50 a resolution structure of ipad from shigella flexneri in complex with single-domain antibody jmk-E3
Analyse 2.50 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
- 5VXJ
- Type
- protein
- Length
- 1,955 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Invasin ipad; Single-domain antibody jmk-E3
- UniProt
- P18013
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 8 distinct chains · 57% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Invasin ipad | protein | 280 | 70% helix, 8% strand | P18013 |
| B, H | Single-domain antibody jmk-E3 | protein | 119 | 8% helix, 54% strand | — |
| C | Invasin ipad | protein | 273 | 71% helix, 8% strand | P18013 |
| D, F | Single-domain antibody jmk-E3 | protein | 118 | 8% helix, 55% strand | — |
| E | Invasin ipad | protein | 278 | 70% helix, 9% strand | P18013 |
| G | Invasin ipad | protein | 274 | 68% helix, 10% strand | P18013 |
| I | Invasin ipad | protein | 259 | 73% helix, 8% strand | P18013 |
| J | Single-domain antibody jmk-E3 | protein | 117 | 8% helix, 53% strand | — |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 799 | 0.74 | 0.79 | 79 | empty |
| 2 | 805 | 0.73 | 0.78 | 78 | empty |
| 3 | 724 | 0.72 | 0.79 | 76 | empty |
| 4 | 739 | 0.72 | 0.78 | 75 | empty |
| 5 | 697 | 0.71 | 0.78 | 66 | empty |
Interfaces
13 interfaces between chains.
- I–J · 939 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 891 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 885 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 877 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 874 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5VXJ · 2.50 A resolution structure of IpaD from Shigella flexneri in complex with single-domain… · the same entry in another collection · chain J against J, TM-score 1.00
- P18013 · AlphaFold monomer V2.0 prediction for invasin ipad (P18013) · a predicted model of the same protein · chain I against A, TM-score 0.99
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 5VXJ · PDBe 5VXJ · UniProt P18013
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