Research workbench
Crystal structure of anti-gliadin 1002-1E01 Fab fragment
Analyse Crystal structure of anti-gliadin 1002-1E01 Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IHZ
- Type
- protein
- Length
- 1,690 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1E01 Fab fragment heavy chain; 1E01 Fab fragment light chain
- Pockets
- 20 · best druggability 0.63
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1E01 Fab fragment heavy chain | protein | 208 | 10% helix, 51% strand | — |
| B, D, F | 1E01 Fab fragment light chain | protein | 213 | 6% helix, 53% strand | — |
| C | 1E01 Fab fragment heavy chain | protein | 208 | 7% helix, 52% strand | — |
| E | 1E01 Fab fragment heavy chain | protein | 209 | 7% helix, 51% strand | — |
| H | 1E01 Fab fragment heavy chain | protein | 211 | 9% helix, 51% strand | — |
| L | 1E01 Fab fragment light chain | protein | 215 | 7% helix, 51% strand | — |
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 645 | 0.63 | 0.74 | 73 | empty |
| 2 | 462 | 0.63 | 0.77 | 68 | empty |
| 3 | 414 | 0.63 | 0.78 | 57 | empty |
| 4 | 301 | 0.61 | 0.79 | 47 | empty |
| 5 | 317 | 0.59 | 0.78 | 45 | empty |
Interfaces
10 interfaces between chains.
- H–L · 1659 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1607 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1594 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1575 Ų buried · 10 hydrogen bonds · protein-protein
- E–H · 714 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 5IHZ · Crystal structure of anti-gliadin 1002-1E01 Fab fragment · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 5IHZ · PDBe 5IHZ
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