Research workbench
Unbound antigen-binding fragment (Fab) 324
Analyse Unbound antigen-binding fragment (Fab) 324 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NX2
- Type
- protein
- Length
- 858 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 324 light chain; Fab 324 heavy chain
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab 324 light chain | protein | 210 | 6% helix, 54% strand | — |
| B, D | Fab 324 heavy chain | protein | 216 | 10% helix, 53% strand | — |
| C | Fab 324 light chain | protein | 216 | 6% helix, 53% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.67 | 0.75 | 83 | SO4 |
| 2 | 732 | 0.66 | 0.74 | 86 | empty |
| 3 | 87 | 0.53 | 0.85 | 25 | empty |
| 4 | 69 | 0.49 | 0.85 | 21 | empty |
| 5 | 96 | 0.36 | 0.75 | 20 | SO4 |
Interfaces
5 interfaces between chains.
- C–D · 1812 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1795 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 336 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 133 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 61 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7NX2 · Unbound antigen-binding fragment (FAb) 324 · the same entry in another collection · chain B against B, 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 7NX2 · PDBe 7NX2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.