MolNFT v1 · #157267 · protein
Crystal structure of VRC42.N1 Fab in complex with T117-F mper scaffold
6MTQ · Antibody VRC42.N1 Fab light chain: “Crystal structure of VRC42.N1 Fab in complex with T117-F mper scaffold”. X-ray diffraction, 6 pockets (best druggability 0.57). MolNFT v1 #157267 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6MTQ
- Type
- protein
- Length
- 589 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody VRC42.N1 Fab light chain; Antibody VRC42.N1 Fab heavy chain; VRC42 epitope…
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Antibody VRC42.N1 Fab light chain | protein | 212 | 8% helix, 54% strand | — |
| H | Antibody VRC42.N1 Fab heavy chain | protein | 221 | 7% helix, 54% strand | — |
| T | VRC42 epitope T117-F scaffold | protein | 156 | 44% helix, 24% strand | — |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.57 | 0.74 | 50 | empty |
| 2 | 113 | 0.46 | 0.79 | 20 | empty |
| 3 | 160 | 0.43 | 0.75 | 30 | empty |
| 4 | 114 | 0.41 | 0.76 | 20 | empty |
| 5 | 75 | 0.32 | 0.74 | 19 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1688 Ų buried · 16 hydrogen bonds · protein-protein
- H–T · 947 Ų buried · 5 hydrogen bonds · protein-protein
- L–T · 248 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6MTQ · Crystal structure of VRC42.N1 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 6MTQ · PDBe 6MTQ
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