Research workbench
Structure of DC8E8 Fab at pH 6.5 crystallized in space-group P1
Analyse Structure of DC8E8 Fab at pH 6.5 crystallized in space-group P1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MVJ
- Type
- protein
- Length
- 1,741 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab heavy chain; Antibody kappa chain
- Ligands
- CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Antibody Fab heavy chain | protein | 219 | 5% helix, 53% strand | — |
| L | Antibody kappa chain | protein | 219 | 6% helix, 53% strand | — |
| A | Antibody Fab heavy chain | protein | 219 | 5% helix, 53% strand | — |
| B, D, F | Antibody kappa chain | protein | 218 | 6% helix, 52% strand | — |
| C | Antibody Fab heavy chain | protein | 214 | 4% helix, 53% strand | — |
| E | Antibody Fab heavy chain | protein | 216 | 9% helix, 52% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.79 | 0.84 | 75 | empty |
| 2 | 1015 | 0.75 | 0.78 | 101 | empty |
| 3 | 795 | 0.67 | 0.75 | 71 | empty |
| 4 | 480 | 0.65 | 0.77 | 55 | empty |
| 5 | 445 | 0.63 | 0.77 | 53 | empty |
Interfaces
16 interfaces between chains.
- H–L · 1998 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1853 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1834 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1825 Ų buried · 14 hydrogen bonds · protein-protein
- L–A · 363 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 modified (disulfide, cyclization).
Compared structures
- 5MVJ · Structure of DC8E8 Fab at pH 6.5 crystallized in space-group P1 · the same entry in another collection · chain H against H, 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 5MVJ · PDBe 5MVJ
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