Research workbench
Structure of GII.4 P-domain in complex with noro-320 Fab
Analyse Structure of GII.4 P-domain in complex with noro-320 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JIE
- Type
- protein
- Length
- 1,500 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; IgA Fab heavy chain; IgA Fab light chain
- UniProt
- K4LM89
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | VP1 | protein | 307 | 6% helix, 35% strand | K4LM89 |
| C | IgA Fab heavy chain | protein | 224 | 8% helix, 50% strand | — |
| D, F | IgA Fab light chain | protein | 217 | 6% helix, 51% strand | — |
| E | IgA Fab heavy chain | protein | 228 | 8% helix, 47% strand | — |
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.75 | 0.88 | 43 | empty |
| 2 | 111 | 0.74 | 0.94 | 21 | empty |
| 3 | 61 | 0.74 | 0.99 | 20 | empty |
| 4 | 1071 | 0.74 | 0.77 | 105 | empty |
| 5 | 262 | 0.74 | 0.87 | 44 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1883 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1844 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1783 Ų buried · 23 hydrogen bonds · protein-protein
- B–E · 493 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 476 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7JIE · Structure of GII.4 P-domain in Complex with NORO-320 FAB · the same entry in another collection · chain B against B, TM-score 1.00
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 K4LM89
- Elsewhere: RCSB PDB 7JIE · PDBe 7JIE · UniProt K4LM89
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