MolNFT v1 · #122269 · protein
Crystal structure of anti-gliadin 1002-1E03 Fab fragment
5IK3 · 1E03 Fab fragment heavy chain: “Crystal structure of anti-gliadin 1002-1E03 Fab fragment”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.72). MolNFT v1 #122269 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5IK3
- Type
- protein
- Length
- 883 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1E03 Fab fragment heavy chain; 1E03 Fab fragment light chain
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1E03 Fab fragment heavy chain | protein | 220 | 13% helix, 50% strand | — |
| B | 1E03 Fab fragment light chain | protein | 220 | 7% helix, 51% strand | — |
| C | 1E03 Fab fragment heavy chain | protein | 225 | 9% helix, 48% strand | — |
| D | 1E03 Fab fragment light chain | protein | 218 | 6% helix, 51% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 796 | 0.72 | 0.78 | 85 | empty |
| 2 | 604 | 0.68 | 0.78 | 61 | SO4 |
| 3 | 112 | 0.61 | 0.87 | 36 | SO4 |
| 4 | 52 | 0.56 | 0.91 | 23 | empty |
| 5 | 128 | 0.45 | 0.77 | 24 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1932 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1913 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 967 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 12 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5IK3 · Crystal structure of anti-gliadin 1002-1E03 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 5IK3 · PDBe 5IK3
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