Research workbench
Crystallographic refinement of the three-dimensional structure of the Fab D1.3-lysozyme complex at 2.5- ångströms resolution
Analyse Crystallographic refinement of the three-dimensional structure of the Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FDL
- Type
- protein
- Length
- 561 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG1-kappa D1.3 Fab (light chain); IGG1-kappa D1.3 Fab (heavy chain); Hen egg white…
- EC
- 3.2.1.17
- UniProt
- P00698
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IGG1-kappa D1.3 Fab (light chain) | protein | 214 | 6% helix, 50% strand | — |
| H | IGG1-kappa D1.3 Fab (heavy chain) | protein | 218 | 6% helix, 51% strand | — |
| Y | Hen egg white lysozyme (EC 3.2.1.17) | protein | 129 | 40% helix, 12% strand | P00698 |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.69 | 0.93 | 18 | empty |
| 2 | 252 | 0.52 | 0.75 | 33 | empty |
| 3 | 293 | 0.50 | 0.73 | 40 | empty |
| 4 | 65 | 0.36 | 0.78 | 16 | empty |
| 5 | 82 | 0.34 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1917 Ų buried · 26 hydrogen bonds · protein-protein
- H–Y · 399 Ų buried · 12 hydrogen bonds · protein-protein
- L–Y · 329 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 1FDL · Crystallographic refinement of the three-dimensional structure of the Fab D1.3-lysozyme… · 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 P00698
- Elsewhere: RCSB PDB 1FDL · PDBe 1FDL · UniProt P00698
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.