MolNFT v1 · #56756 · protein
Crystal structure of P20.1 Fab fragment in complex with its antigen peptide
2ZPK · IGG1-lambda P20.1 Fab (light chain): “Crystal structure of P20.1 Fab fragment in complex with its antigen peptide”. X-ray diffraction, 10 pockets (best druggability 0.68). MolNFT v1 #56756 on GenesisL1: 3D structure, binding sites…
- 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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