MolNFT v1 · #97700 · protein
Crystal structure of human germline antibody 5-51/O12
4KMT · Light chain O12/KAPPA: “Crystal structure of human germline antibody 5-51/O12”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.58). MolNFT v1 #97700 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4KMT
- Type
- protein
- Length
- 432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain O12/KAPPA; Heavy chain 5-51/CNTO888/IGG1
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Light chain O12/KAPPA | protein | 214 | 6% helix, 50% strand | — |
| H | Heavy chain 5-51/CNTO888/IGG1 | protein | 218 | 8% helix, 51% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains L, H
- GOL · Glycerol · additive · 7 copies · chains L, H
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 3 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.58 | 0.75 | 55 | empty |
| 2 | 223 | 0.54 | 0.77 | 34 | NHE, GOL |
| 3 | 54 | 0.46 | 0.85 | 23 | GOL |
| 4 | 90 | 0.34 | 0.74 | 20 | empty |
| 5 | 75 | 0.33 | 0.75 | 17 | SO4 |
Interfaces
1 interface between chains.
- L–H · 1861 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4KMT · Crystal structure of human germline antibody 5-51/O12 · 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 4KMT · PDBe 4KMT
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