MolNFT v1 · #167475 · protein
Crystal structure of 426COD in complex with VRC01 Fab
6VLW · VRC01 Fab heavy chain: “Crystal structure of 426COD in complex with VRC01 Fab”. X-ray diffraction, 5 ligands (NAG, BMA, NA), 6 pockets (best druggability 0.43). MolNFT v1 #167475 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6VLW
- Type
- protein
- Length
- 597 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VRC01 Fab heavy chain; VRC01 Fab light chain; 426COD
- Ligands
- NAG, BMA, NA, CL, SO4
- Pockets
- 6 · best druggability 0.43
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | VRC01 Fab heavy chain | protein | 217 | 10% helix, 57% strand | — |
| L | VRC01 Fab light chain | protein | 210 | 7% helix, 45% strand | — |
| G | 426COD | protein | 170 | 21% helix, 35% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains L, G
- BMA · beta-D-mannopyranose · sugar
- NA · Sodium ion · metal · chains L
- CL · Chloride ion · ion · 8 copies · chains H, L, G
- SO4 · Sulfate ion · ion · 2 copies · chains H, L, G
- EDO · 1,2-ethanediol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.43 | 0.79 | 19 | empty |
| 2 | 169 | 0.43 | 0.73 | 30 | empty |
| 3 | 109 | 0.34 | 0.73 | 23 | empty |
| 4 | 51 | 0.34 | 0.78 | 14 | empty |
| 5 | 81 | 0.30 | 0.72 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1699 Ų buried · 8 hydrogen bonds · protein-protein
- H–G · 937 Ų buried · 16 hydrogen bonds · protein-protein
- L–G · 292 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 4 glycan, 1 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 6VLW · Crystal Structure of 426cOD in Complex with VRC01 Fab · the same entry in another collection · chain H against H, 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 6VLW · PDBe 6VLW
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.