Research workbench
Crystal structure of VRC46.01 Fab in complex with GP41 peptide
Analyse Crystal structure of VRC46.01 Fab in complex with GP41 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MTT
- Type
- protein
- Length
- 450 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody VRC46.01 fb light chain; Antibody VRC46.01 Fab heavy chain; RV217 founder virus…
- UniProt
- A0A0U3UAX4
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Antibody VRC46.01 fb light chain | protein | 211 | 6% helix, 51% strand | — |
| H | Antibody VRC46.01 Fab heavy chain | protein | 220 | 8% helix, 50% strand | — |
| P | RV217 founder virus GP41 peptide | protein | 19 | 26% helix, 11% strand | A0A0U3UAX4 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.48 | 0.86 | 20 | empty |
| 2 | 90 | 0.34 | 0.74 | 21 | empty |
| 3 | 63 | 0.28 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1841 Ų buried · 15 hydrogen bonds · protein-protein
- H–P · 1056 Ų buried · 17 hydrogen bonds · protein-protein
- L–P · 131 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6MTT · Crystal structure of VRC46.01 Fab in complex with gp41 peptide · 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
- Every structure of UniProt A0A0U3UAX4
- Elsewhere: RCSB PDB 6MTT · PDBe 6MTT · UniProt A0A0U3UAX4
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