MolNFT v1 · #139133 · protein
Crystal structure of the Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219
5X5X · Fd chain of anti-osteocalcin antibody KTM219: “Crystal structure of the Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219”. X-ray diffraction, 5 pockets (best druggability 0.64). MolNFT v1 #139133 on GenesisL1: 3D…
- PDB
- 5X5X
- Type
- protein
- Length
- 433 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fd chain of anti-osteocalcin antibody KTM219; L chain of anti-osteocalcin antibody KTM219
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fd chain of anti-osteocalcin antibody KTM219 | protein | 216 | 8% helix, 54% strand | — |
| L | L chain of anti-osteocalcin antibody KTM219 | protein | 217 | 6% helix, 51% strand | — |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains H, L
- FMT · Formic acid · additive · 3 copies · chains H, L
- PG4 · Tetraethylene glycol · additive · 2 copies · chains H, L
- PGE · Triethylene glycol · additive · 2 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.64 | 0.83 | 31 | PG4, PGE |
| 2 | 60 | 0.47 | 0.85 | 22 | empty |
| 3 | 144 | 0.37 | 0.72 | 28 | PGE |
| 4 | 83 | 0.35 | 0.75 | 18 | empty |
| 5 | 66 | 0.31 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- H–L · 1684 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5X5X · Crystal structure of the Fab fragment of anti-osteocalcin C-terminal peptide antibody… · 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 5X5X · PDBe 5X5X
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.