MolNFT v1 · #156792 · protein
Crystal structure of the adcc potent antibody DH677.3 Fab elicited in the RV305 vaccine trial.
6MFJ · DH677.3 Fab heavy chain: “Crystal structure of the adcc potent antibody DH677.3 Fab elicited in the RV305 vaccine trial.”. X-ray diffraction, 1 ligand (NAG), 13 pockets (best druggability 0.64). MolNFT v1 #156792 on GenesisL1: 3D…
- 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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