Research workbench
Structure of the apo 4497 antibody Fab fragment
Analyse Structure of the apo 4497 antibody Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DWC
- Type
- protein
- Length
- 864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4497 Fab light chain; 4497 Fab heavy chain
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4497 Fab light chain | protein | 217 | 6% helix, 52% strand | — |
| B | 4497 Fab heavy chain | protein | 212 | 8% helix, 50% strand | — |
| H | 4497 Fab heavy chain | protein | 215 | 7% helix, 49% strand | — |
| L | 4497 Fab light chain | protein | 220 | 6% helix, 51% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 715 | 0.68 | 0.76 | 74 | empty |
| 2 | 738 | 0.66 | 0.74 | 74 | ACT |
| 3 | 564 | 0.61 | 0.74 | 50 | empty |
| 4 | 284 | 0.58 | 0.78 | 39 | GOL |
| 5 | 126 | 0.37 | 0.74 | 19 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1876 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1741 Ų buried · 15 hydrogen bonds · protein-protein
- A–L · 644 Ų buried · 11 hydrogen bonds · protein-protein
- A–H · 74 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 6DWC · Structure of the apo 4497 antibody Fab fragment · the same entry in another collection · chain A against A, 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 6DWC · PDBe 6DWC
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