MolNFT v1 · #122134 · protein
Crystal structure of anti-gliadin 1002-1E01 Fab fragment in complex of peptide plqpqqpfp
5IG7 · 1E01 Fab fragment heavy chain: “Crystal structure of anti-gliadin 1002-1E01 Fab fragment in complex of peptide plqpqqpfp”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.70). MolNFT v1 #122134 on GenesisL1: 3D…
- PDB
- 5IG7
- Type
- protein
- Length
- 1,756 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 0.70
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | 1E01 Fab fragment heavy chain | protein | 216 | 8% helix, 50% strand | — |
| B, E, H, K | 1E01 Fab fragment light chain | protein | 213 | 7% helix, 53% strand | — |
| C, F, I, L | Peptide pro-leu-gln-pro-gln-gln-pro-phe-pro | protein | 9 | 0% helix, 0% strand | — |
| D | 1E01 Fab fragment heavy chain | protein | 217 | 7% helix, 49% strand | — |
| J | 1E01 Fab fragment heavy chain | protein | 219 | 8% helix, 49% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, D, G, E, F, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 887 | 0.70 | 0.75 | 99 | empty |
| 2 | 554 | 0.61 | 0.74 | 52 | empty |
| 3 | 370 | 0.61 | 0.77 | 51 | empty |
| 4 | 349 | 0.60 | 0.77 | 53 | empty |
| 5 | 298 | 0.58 | 0.77 | 43 | empty |
Interfaces
19 interfaces between chains.
- A–B · 1722 Ų buried · 18 hydrogen bonds · protein-protein
- J–K · 1711 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1702 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 1702 Ų buried · 15 hydrogen bonds · protein-protein
- A–G · 732 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 5IG7 · Crystal structure of anti-gliadin 1002-1E01 Fab fragment in complex of peptide PLQPQQPFP · 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 5IG7 · PDBe 5IG7
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