MolNFT v1 · #12106 · protein
Crystal structure of antibody Fab fragment D3
1K6Q · Immunoglobulin Fab D3, light chain: “Crystal structure of antibody Fab fragment D3”. X-ray diffraction, 3 pockets (best druggability 0.72). MolNFT v1 #12106 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1K6Q
- Type
- protein
- Length
- 417 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin Fab D3, light chain; Immunoglobulin Fab D3, heavy chain
- UniProt
- Q9R1A5
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Immunoglobulin Fab D3, light chain | protein | 204 | 5% helix, 50% strand | Q9R1A5 |
| H | Immunoglobulin Fab D3, heavy chain | protein | 213 | 9% helix, 52% strand | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 737 | 0.72 | 0.78 | 67 | empty |
| 2 | 109 | 0.39 | 0.75 | 19 | empty |
| 3 | 74 | 0.30 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- L–H · 1848 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1K6Q · Crystal structure of antibody Fab fragment D3 · 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 Q9R1A5
- Elsewhere: RCSB PDB 1K6Q · PDBe 1K6Q · UniProt Q9R1A5
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