MolNFT v1 · #122251 · protein
Crystal structure of anti-gliadin 1002-1E03 Fab fragment in complex of peptide plqpeqpfp
5IJK · Peptide pro-leu-gln-pro-glu-gln-pro-phe-pro: “Crystal structure of anti-gliadin 1002-1E03 Fab fragment in complex of peptide plqpeqpfp”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.71). MolNFT v1 #122251 on…
- PDB
- 5IJK
- Type
- protein
- Length
- 877 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide pro-leu-gln-pro-glu-gln-pro-phe-pro; 1E03 Fab fragment heavy chain; 1E03 Fab…
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Peptide pro-leu-gln-pro-glu-gln-pro-phe-pro | protein | 8 | 0% helix, 0% strand | — |
| Y | Peptide pro-leu-gln-pro-glu-gln-pro-phe-pro | protein | 9 | 0% helix, 0% strand | — |
| A | 1E03 Fab fragment heavy chain | protein | 213 | 6% helix, 47% strand | — |
| B | 1E03 Fab fragment heavy chain | protein | 211 | 7% helix, 47% strand | — |
| C, D | 1E03 Fab fragment light chain | protein | 218 | 6% helix, 50% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, Y, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.71 | 0.80 | 70 | SO4 |
| 2 | 639 | 0.70 | 0.78 | 64 | empty |
| 3 | 396 | 0.61 | 0.77 | 66 | empty |
| 4 | 131 | 0.50 | 0.80 | 30 | empty |
| 5 | 55 | 0.25 | 0.73 | 20 | empty |
Interfaces
10 interfaces between chains.
- B–D · 1673 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1646 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 785 Ų buried · 10 hydrogen bonds · protein-protein
- Y–D · 397 Ų buried · 3 hydrogen bonds · protein-protein
- X–C · 381 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5IJK · Crystal structure of anti-gliadin 1002-1E03 Fab fragment in complex of peptide PLQPEQPFP · the same entry in another collection · chain X against X, 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 5IJK · PDBe 5IJK
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