Research workbench
Crystal structure of anti-gliadin 1002-1E01 Fab fragment in complex of peptide PLQPEQPFP
Analyse Crystal structure of anti-gliadin 1002-1E01 Fab fragment in complex of peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IFJ
- Type
- protein
- Length
- 1,755 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.35
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- 1E01 Fab fragment heavy chain; 1E01 Fab fragment light chain; peptide…
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.62
Structure
x-ray diffraction · resolution 2.35 · 6 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1E01 Fab fragment heavy chain | protein | 216 | 7% helix, 49% strand | — |
| B, E, H, K | 1E01 Fab fragment light chain | protein | 213 | 7% helix, 52% strand | — |
| C, F, I, L | peptide PRO-LEU-GLN-PRO-GLU-GLN-PRO-PHE-PRO | protein | 9 | 0% helix, 0% strand | — |
| D | 1E01 Fab fragment heavy chain | protein | 217 | 7% helix, 49% strand | — |
| G | 1E01 Fab fragment heavy chain | protein | 215 | 7% helix, 48% strand | — |
| J | 1E01 Fab fragment heavy chain | protein | 219 | 7% helix, 49% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D, E, G, H, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.62 | 0.78 | 66 | empty |
| 2 | 358 | 0.61 | 0.78 | 51 | empty |
| 3 | 348 | 0.60 | 0.78 | 53 | empty |
| 4 | 328 | 0.57 | 0.76 | 43 | empty |
| 5 | 388 | 0.54 | 0.73 | 47 | empty |
Interfaces
20 interfaces between chains.
- D–E · 1779 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 1757 Ų buried · 20 hydrogen bonds · protein-protein
- J–K · 1701 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1686 Ų buried · 20 hydrogen bonds · protein-protein
- D–J · 751 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 5IFJ · Crystal structure of anti-gliadin 1002-1E01 Fab fragment in complex of peptide plqpeqpfp · 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 5IFJ · PDBe 5IFJ
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