Research workbench
Crystal structure of LN01 Fab in complex with an HIV-1 GP41 peptide
Analyse Crystal structure of LN01 Fab in complex with an HIV-1 GP41 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SND
- Type
- protein
- Length
- 918 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LN01 light chain; LN01 heavy chain; Envelope glycoprotein GP160
- UniProt
- G3DH64
- Ligands
- DPV, PC, PSF, NAG
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | LN01 light chain | protein | 213 | 7% helix, 52% strand | — |
| B | LN01 heavy chain | protein | 230 | 8% helix, 49% strand | — |
| C, P | Envelope glycoprotein GP160 | protein | 19 | 89% helix, 0% strand | G3DH64 |
| H | LN01 heavy chain | protein | 224 | 7% helix, 49% strand | — |
Ligands and binding sites
- DPV · dodecyl 2-(trimethylammonio)ethyl phosphate · ligand · chains A, B, C
- PC · Phosphocholine · ligand · chains B, L, H, P
- PSF · 1,2-dicaproyl-sn-phosphatidyl-L-serine · ligand · chains H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.77 | 0.79 | 102 | PC |
| 2 | 767 | 0.67 | 0.75 | 59 | empty |
| 3 | 301 | 0.59 | 0.78 | 35 | empty |
| 4 | 73 | 0.48 | 0.83 | 24 | empty |
| 5 | 156 | 0.47 | 0.77 | 26 | empty |
Interfaces
11 interfaces between chains.
- A–B · 2136 Ų buried · 14 hydrogen bonds · protein-protein
- L–H · 1899 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 504 Ų buried · 3 hydrogen bonds · protein-protein
- H–P · 503 Ų buried · 3 hydrogen bonds · protein-protein
- B–L · 324 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6SND · crystal structure of LN01 Fab in complex with an HIV-1 gp41 peptide · 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
- Every structure of UniProt G3DH64
- Elsewhere: RCSB PDB 6SND · PDBe 6SND · UniProt G3DH64
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.