MolNFT v1 · #122113 · protein
Crystal structure of anti-gliadin 1002-1E01 Fab fragment in complex of peptide plqpeqpfp
5IFJ · 1E01 Fab fragment heavy chain: “Crystal structure of anti-gliadin 1002-1E01 Fab fragment in complex of peptide plqpeqpfp”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.62). MolNFT v1 #122113 on GenesisL1: 3D…
- PDB
- 5IFJ
- Type
- protein
- Length
- 1,755 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1E01 Fab fragment heavy chain; 1E01 Fab fragment light chain; Peptide…
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.62
Structure
x-ray diffraction · 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 D against D, 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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