Research workbench
Germline V-genes sculpt the binding site of a family of antibodies neutralizing human cytomegalovirus
Analyse Germline V-genes sculpt the binding site of a family of antibodies neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F12
- Type
- protein
- Length
- 825 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M2J1 Fab; 8F9 Fab
- Pockets
- 8 · best druggability 0.44
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M2J1 Fab | protein | 211 | 2% helix, 47% strand | — |
| B | 8F9 Fab | protein | 199 | 0% helix, 44% strand | — |
| C | M2J1 Fab | protein | 213 | 5% helix, 45% strand | — |
| D | 8F9 Fab | protein | 202 | 4% helix, 49% strand | — |
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.44 | 0.74 | 39 | empty |
| 2 | 203 | 0.43 | 0.73 | 30 | empty |
| 3 | 103 | 0.38 | 0.75 | 27 | empty |
| 4 | 92 | 0.37 | 0.76 | 18 | empty |
| 5 | 91 | 0.37 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1714 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1691 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 566 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3F12 · Germline V-genes sculpt the binding site of a family of antibodies neutralizing human… · 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 3F12 · PDBe 3F12
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