Research workbench
Crystal structure of 5C4 Fab
Analyse Crystal structure of 5C4 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W24
- Type
- protein
- Length
- 431 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5C4 Fab light chain; 5C4 Fab heavy chain
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | 5C4 Fab light chain | protein | 215 | 6% helix, 55% strand | — |
| H | 5C4 Fab heavy chain | protein | 216 | 8% helix, 54% strand | — |
Ligands and binding sites
- BU3 · (R,R)-2,3-butanediol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.68 | 0.76 | 61 | empty |
| 2 | 84 | 0.34 | 0.74 | 21 | empty |
| 3 | 78 | 0.33 | 0.75 | 17 | empty |
| 4 | 75 | 0.32 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- L–H · 1918 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5W24 · Crystal Structure of 5C4 Fab · 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 5W24 · PDBe 5W24
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