MolNFT v1 · #146392 · protein
Antigen binding fragment of the pan-ebolavirus monoclonal antibody 6D6
6DG2 · 6D6 Fab heavy chain: “Antigen binding fragment of the pan-ebolavirus monoclonal antibody 6D6”. X-ray diffraction, 9 pockets (best druggability 0.62). MolNFT v1 #146392 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6DG2
- Type
- protein
- Length
- 851 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6D6 Fab heavy chain; 6D6 Fab light chain
- Pockets
- 9 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6D6 Fab heavy chain | protein | 217 | 10% helix, 51% strand | — |
| B | 6D6 Fab light chain | protein | 212 | 6% helix, 49% strand | — |
| C | 6D6 Fab heavy chain | protein | 211 | 9% helix, 48% strand | — |
| D | 6D6 Fab light chain | protein | 211 | 6% helix, 48% strand | — |
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.62 | 0.80 | 44 | empty |
| 2 | 450 | 0.61 | 0.76 | 57 | empty |
| 3 | 480 | 0.60 | 0.75 | 61 | empty |
| 4 | 54 | 0.53 | 0.89 | 20 | empty |
| 5 | 51 | 0.52 | 0.89 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1654 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1569 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 336 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 151 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 140 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6DG2 · Antigen Binding Fragment of the Pan-ebolavirus Monoclonal Antibody 6D6 · the same entry in another collection · chain A against A, 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 6DG2 · PDBe 6DG2
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