Research workbench
Crystal structure of VRC42.01 Fab in complex with T117-F mper scaffold
Analyse Crystal structure of VRC42.01 Fab in complex with T117-F mper scaffold in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MTO
- Type
- protein
- Length
- 588 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody VRC42.01 Fab light chain; Antibody VRC42.01 Fab heavy chain; VRC42 epitope…
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Antibody VRC42.01 Fab light chain | protein | 212 | 8% helix, 50% strand | — |
| H | Antibody VRC42.01 Fab heavy chain | protein | 219 | 7% helix, 54% strand | — |
| T | VRC42 epitope T117-F scaffold | protein | 157 | 43% helix, 22% strand | — |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.58 | 0.74 | 50 | empty |
| 2 | 219 | 0.54 | 0.78 | 27 | empty |
| 3 | 130 | 0.43 | 0.76 | 20 | empty |
| 4 | 130 | 0.42 | 0.75 | 23 | empty |
| 5 | 108 | 0.39 | 0.75 | 21 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1725 Ų buried · 8 hydrogen bonds · protein-protein
- H–T · 862 Ų buried · 6 hydrogen bonds · protein-protein
- L–T · 197 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6MTO · Crystal structure of VRC42.01 Fab in complex with T117-F MPER scaffold · 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 6MTO · PDBe 6MTO
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.