MolNFT v1 · #134334 · protein
2A10 antibody Fab fragment
5T0Y · 2A10 Fab fragment light chain: “2A10 antibody Fab fragment”. X-ray diffraction, 1 ligand (SO4), 13 pockets (best druggability 0.75). MolNFT v1 #134334 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5T0Y
- Type
- protein
- Length
- 1,286 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2A10 Fab fragment light chain; 2A10 Fab fragment heavy chain
- Ligands
- SO4
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, B | 2A10 Fab fragment light chain | protein | 212 | 5% helix, 50% strand | — |
| H, A, I | 2A10 Fab fragment heavy chain | protein | 217 | 6% helix, 51% strand | — |
| G | 2A10 Fab fragment light chain | protein | 211 | 5% helix, 49% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 18 copies · chains L, H, B, A, G, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.75 | 0.78 | 122 | empty |
| 2 | 333 | 0.54 | 0.74 | 56 | empty |
| 3 | 151 | 0.44 | 0.75 | 24 | empty |
| 4 | 181 | 0.43 | 0.74 | 26 | empty |
| 5 | 137 | 0.43 | 0.75 | 19 | empty |
Interfaces
5 interfaces between chains.
- G–I · 1923 Ų buried · 18 hydrogen bonds · protein-protein
- L–H · 1909 Ų buried · 18 hydrogen bonds · protein-protein
- B–A · 1870 Ų buried · 21 hydrogen bonds · protein-protein
- L–B · 501 Ų buried · 6 hydrogen bonds · protein-protein
- H–A · 189 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5T0Y · 2A10 Antibody 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
- Elsewhere: RCSB PDB 5T0Y · PDBe 5T0Y
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