MolNFT v1 · #40380 · protein
PFA1 Fab fragment
2IPT · IGG2A Fab fragment heavy chain: “PFA1 Fab fragment”. X-ray diffraction, 1 ligand (ACM), 6 pockets (best druggability 0.51). MolNFT v1 #40380 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2IPT
- Type
- protein
- Length
- 442 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG2A Fab fragment heavy chain; IGG2A Fab fragment light chain kappa
- UniProt
- A2NHM3, Q6PIP8
- Ligands
- ACM
- Pockets
- 6 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IGG2A Fab fragment heavy chain | protein | 219 | 8% helix, 51% strand | A2NHM3 |
| H | IGG2A Fab fragment light chain kappa | protein | 223 | 7% helix, 49% strand | Q6PIP8 |
Ligands and binding sites
- ACM · Acetamide · ligand · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.51 | 0.74 | 47 | empty |
| 2 | 96 | 0.47 | 0.80 | 16 | empty |
| 3 | 101 | 0.39 | 0.76 | 16 | empty |
| 4 | 69 | 0.30 | 0.73 | 18 | empty |
| 5 | 52 | 0.27 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- L–H · 1887 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 2IPT · PFA1 Fab Fragment · the same entry in another collection · chain L against L, 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
- Every structure of UniProt A2NHM3
- Every structure of UniProt Q6PIP8
- Elsewhere: RCSB PDB 2IPT · PDBe 2IPT · UniProt A2NHM3 · UniProt Q6PIP8
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