Research workbench
Crystal structure of murine 12F4 Fab monoclonal antibody against ADAMTS5
Analyse Crystal structure of murine 12F4 Fab monoclonal antibody against ADAMTS5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X8J
- Type
- protein
- Length
- 830 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 12F4 Fab light chain; 12F4 Fab heavy chain
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, B | 12F4 Fab light chain | protein | 214 | 7% helix, 49% strand | — |
| H | 12F4 Fab heavy chain | protein | 203 | 8% helix, 50% strand | — |
| A | 12F4 Fab heavy chain | protein | 199 | 8% helix, 51% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains H
- 2PE · Nonaethylene glycol · additive · 2 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.76 | 0.78 | 69 | empty |
| 2 | 537 | 0.75 | 0.83 | 64 | empty |
| 3 | 246 | 0.47 | 0.73 | 41 | empty |
| 4 | 102 | 0.40 | 0.76 | 14 | empty |
| 5 | 108 | 0.40 | 0.76 | 17 | empty |
Interfaces
4 interfaces between chains.
- L–H · 1821 Ų buried · 16 hydrogen bonds · protein-protein
- B–A · 1795 Ų buried · 20 hydrogen bonds · protein-protein
- L–B · 636 Ų buried · 14 hydrogen bonds · protein-protein
- L–A · 155 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 4X8J · Crystal Structure of murine 12F4 Fab monoclonal antibody against ADAMTS5 · 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 4X8J · PDBe 4X8J
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