MolNFT v1 · #157927 · protein
Fab fragment of anti-cocaine antibody H2E2
6NEX · Anitgen binding fragment light chain: “Fab fragment of anti-cocaine antibody H2E2”. X-ray diffraction, 1 ligand (CL), 10 pockets (best druggability 0.63). MolNFT v1 #157927 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6NEX
- Type
- protein
- Length
- 851 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anitgen binding fragment light chain; Antigen binding fragment heavy chain
- Ligands
- CL
- Pockets
- 10 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Anitgen binding fragment light chain | protein | 212 | 8% helix, 54% strand | — |
| H, B | Antigen binding fragment heavy chain | protein | 213 | 6% helix, 49% strand | — |
| A | Anitgen binding fragment light chain | protein | 213 | 7% helix, 52% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains L, H, A
- FMT · Formic acid · additive · 4 copies · chains L, A, B
- ACT · Acetate ion · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 649 | 0.63 | 0.74 | 65 | empty |
| 2 | 456 | 0.59 | 0.74 | 46 | empty |
| 3 | 234 | 0.55 | 0.78 | 40 | empty |
| 4 | 292 | 0.55 | 0.76 | 38 | empty |
| 5 | 113 | 0.40 | 0.75 | 25 | empty |
Interfaces
4 interfaces between chains.
- L–H · 1706 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1645 Ų buried · 12 hydrogen bonds · protein-protein
- L–B · 250 Ų buried · 6 hydrogen bonds · protein-protein
- H–B · 80 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 19 modified, 8 disulfide (methylation, disulfide, cyclization).
Compared structures
- 6NEX · Fab fragment of anti-cocaine antibody h2E2 · 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 6NEX · PDBe 6NEX
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