MolNFT v1 · #27282 · protein
Structure of ligand-free Fab DNA-1 in space group P65
1XF3 · Fab light chain: “Structure of ligand-free Fab DNA-1 in space group P65”. X-ray diffraction, 10 pockets (best druggability 0.68). MolNFT v1 #27282 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1XF3
- Type
- protein
- Length
- 860 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab light chain; Fab heavy chain
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Fab light chain | protein | 213 | 7% helix, 50% strand | — |
| H | Fab heavy chain | protein | 216 | 8% helix, 50% strand | — |
| B | Fab heavy chain | protein | 218 | 8% helix, 50% strand | — |
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 | 448 | 0.68 | 0.80 | 59 | empty |
| 2 | 428 | 0.57 | 0.74 | 63 | empty |
| 3 | 425 | 0.57 | 0.74 | 51 | empty |
| 4 | 197 | 0.53 | 0.78 | 30 | empty |
| 5 | 184 | 0.50 | 0.77 | 31 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1793 Ų buried · 16 hydrogen bonds · protein-protein
- L–H · 1740 Ų buried · 15 hydrogen bonds · protein-protein
- H–B · 411 Ų buried · 10 hydrogen bonds · protein-protein
- H–A · 179 Ų buried · 1 hydrogen bond · protein-protein
- L–B · 134 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1XF3 · Structure of ligand-free Fab DNA-1 in space group P65 · 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 1XF3 · PDBe 1XF3
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