MolNFT v1 · #153974 · protein
Mouse antibody 2B5 Fab in complex with peg
6JWC · Immunoglobulin heavy chain Fab fragment: “Mouse antibody 2B5 Fab in complex with peg”. X-ray diffraction, 2 ligands (O4B, SO4), 5 pockets (best druggability 0.62). MolNFT v1 #153974 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6JWC
- Type
- protein
- Length
- 425 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin heavy chain Fab fragment; Immunoglobulin light chain
- Ligands
- O4B, SO4
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Immunoglobulin heavy chain Fab fragment | protein | 213 | 10% helix, 55% strand | — |
| L | Immunoglobulin light chain | protein | 212 | 8% helix, 50% strand | — |
Ligands and binding sites
- O4B · 1,4,7,10,13,16-hexaoxacyclooctadecane · ligand · 5 copies · chains H, L
- SO4 · Sulfate ion · ion · 5 copies · chains H, L
- 12P · Dodecaethylene glycol · additive · chains H, L
- PEG · Di(hydroxyethyl)ether · additive · 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 | 582 | 0.62 | 0.74 | 59 | O4B |
| 2 | 116 | 0.40 | 0.75 | 21 | empty |
| 3 | 78 | 0.33 | 0.74 | 14 | empty |
| 4 | 51 | 0.32 | 0.78 | 17 | empty |
| 5 | 65 | 0.30 | 0.74 | 17 | SO4 |
Interfaces
1 interface between chains.
- H–L · 1837 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 6JWC · Mouse antibody 2B5 Fab in complex with PEG · 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 6JWC · PDBe 6JWC
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