Research workbench
Crystal structure of P20.1 Fab fragment in complex with its antigen peptide
Analyse Crystal structure of P20.1 Fab fragment in complex with its antigen peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZPK
- Type
- protein
- Length
- 853 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG1-lambda P20.1 Fab (light chain); IGG1-lambda P20.1 Fab (heavy chain)…
- UniProt
- Q96RI0
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IGG1-lambda P20.1 Fab (light chain) | protein | 212 | 8% helix, 55% strand | — |
| H | IGG1-lambda P20.1 Fab (heavy chain) | protein | 208 | 7% helix, 51% strand | — |
| P, Q | Proteinase-activated receptor 4 | protein | 8 | 0% helix, 0% strand | Q96RI0 |
| M | IGG1-lambda P20.1 Fab (light chain) | protein | 209 | 8% helix, 55% strand | — |
| I | IGG1-lambda P20.1 Fab (heavy chain) | protein | 208 | 6% helix, 52% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains H, M, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 678 | 0.68 | 0.76 | 67 | empty |
| 2 | 450 | 0.58 | 0.74 | 50 | empty |
| 3 | 73 | 0.37 | 0.77 | 20 | empty |
| 4 | 86 | 0.35 | 0.75 | 17 | empty |
| 5 | 73 | 0.34 | 0.76 | 18 | empty |
Interfaces
7 interfaces between chains.
- L–H · 1831 Ų buried · 8 hydrogen bonds · protein-protein
- M–I · 1700 Ų buried · 7 hydrogen bonds · protein-protein
- L–M · 427 Ų buried · 5 hydrogen bonds · protein-protein
- I–Q · 329 Ų buried · 10 hydrogen bonds · protein-protein
- H–P · 326 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 modified (disulfide, cyclization).
Compared structures
- 2ZPK · Crystal structure of P20.1 Fab fragment in complex with its antigen peptide · the same entry in another collection · chain P against P, TM-score 1.00
- Q96RI0 · AlphaFold monomer V2.0 prediction for proteinase-activated receptor 4 (Q96RI0) · a predicted model of the same protein · chain P against A, TM-score 0.39
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q96RI0
- Elsewhere: RCSB PDB 2ZPK · PDBe 2ZPK · UniProt Q96RI0
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