Research workbench
Crystal structure of the adcc potent antibody DH677.3 Fab elicited in the RV305 vaccine trial.
Analyse Crystal structure of the adcc potent antibody DH677.3 Fab elicited in the RV305… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MFJ
- Type
- protein
- Length
- 861 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DH677.3 Fab heavy chain; DH677.3 Fab light chain
- Ligands
- NAG
- Pockets
- 13 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | DH677.3 Fab heavy chain | protein | 219 | 8% helix, 49% strand | — |
| L | DH677.3 Fab light chain | protein | 213 | 6% helix, 51% strand | — |
| A | DH677.3 Fab heavy chain | protein | 217 | 8% helix, 51% strand | — |
| B | DH677.3 Fab light chain | protein | 212 | 7% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains H, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.64 | 0.79 | 50 | empty |
| 2 | 294 | 0.63 | 0.80 | 40 | empty |
| 3 | 59 | 0.49 | 0.86 | 21 | empty |
| 4 | 104 | 0.48 | 0.81 | 22 | empty |
| 5 | 55 | 0.47 | 0.86 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1802 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 1782 Ų buried · 12 hydrogen bonds · protein-protein
- L–B · 393 Ų buried · 7 hydrogen bonds · protein-protein
- H–A · 272 Ų buried · 4 hydrogen bonds · protein-protein
- H–B · 67 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6MFJ · Crystal structure of the ADCC potent antibody DH677.3 Fab elicited in the RV305 vaccine… · 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 6MFJ · PDBe 6MFJ
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