MolNFT v1 · #164103 · protein
Crystal structure of LN01 Fab in complex with an HIV-1 GP41 peptide
6SNC · LNO1 light chain: “Crystal structure of LN01 Fab in complex with an HIV-1 GP41 peptide”. X-ray diffraction, 4 ligands (PC, DPV, NAG), 7 pockets (best druggability 0.77). MolNFT v1 #164103 on GenesisL1: 3D structure, binding sites…
- PDB
- 6SNC
- Type
- protein
- Length
- 914 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LNO1 light chain; LNO1 heavy chain; Envelope glycoprotein GP160
- UniProt
- G3DH64
- Ligands
- PC, DPV, NAG, PO4
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LNO1 light chain | protein | 213 | 7% helix, 51% strand | — |
| B | LNO1 heavy chain | protein | 230 | 8% helix, 50% strand | — |
| L | LNO1 light chain | protein | 210 | 7% helix, 52% strand | — |
| H | LNO1 heavy chain | protein | 223 | 8% helix, 48% strand | — |
| P, C | Envelope glycoprotein GP160 | protein | 19 | 89% helix, 0% strand | G3DH64 |
Ligands and binding sites
- PC · Phosphocholine · ligand · 2 copies · chains B, L, H, P, A, C
- DPV · dodecyl 2-(trimethylammonio)ethyl phosphate · ligand · chains H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, L
- PO4 · Phosphate ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1179 | 0.77 | 0.79 | 97 | PC |
| 2 | 803 | 0.67 | 0.75 | 70 | empty |
| 3 | 351 | 0.61 | 0.78 | 42 | empty |
| 4 | 145 | 0.45 | 0.76 | 26 | empty |
| 5 | 71 | 0.32 | 0.75 | 17 | empty |
Interfaces
11 interfaces between chains.
- A–B · 2112 Ų buried · 18 hydrogen bonds · protein-protein
- L–H · 1854 Ų buried · 15 hydrogen bonds · protein-protein
- H–P · 497 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 494 Ų buried · 3 hydrogen bonds · protein-protein
- B–L · 312 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6SNC · 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 6SNC · PDBe 6SNC · UniProt G3DH64
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