MolNFT v1 · #145313 · protein
Crystal structure of HIV-1 CONC_BASE0 prefusion env trimer in complex with human antibody fragment 3H109L and 35O22 variants at 3.5 ångström
6CK9 · GP41 ectodomain of envelope glycoprotein GP160: “Crystal structure of HIV-1 CONC_BASE0 prefusion env trimer in complex with human antibody fragment 3H109L and…”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 18 pockets (best…
- PDB
- 6CK9
- Type
- protein
- Length
- 1,217 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GP41 ectodomain of envelope glycoprotein GP160; 35O22 scfv heavy chain portion; 35O22…
- Ligands
- NAG, MAN, BMA
- Pockets
- 18 · best druggability 0.68
Structure
x-ray diffraction · 6 distinct chains · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | GP41 ectodomain of envelope glycoprotein GP160 | protein | 129 | 53% helix, 5% strand | — |
| D | 35O22 scfv heavy chain portion | protein | 128 | 5% helix, 43% strand | — |
| E | 35O22 scfv light chain portion | protein | 100 | 0% helix, 41% strand | — |
| G | GP120 of envelope glycoprotein GP160 | protein | 430 | 11% helix, 36% strand | — |
| H | 3H109L Fab heavy chain | protein | 219 | 3% helix, 49% strand | — |
| L | 3H109L Fab light chain | protein | 211 | 5% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 29 copies · chains G, B, D, L, H
- MAN · alpha-D-mannopyranose · sugar · 13 copies · chains G, D, E, H, L
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains D, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.68 | 0.89 | 27 | NAG |
| 2 | 51 | 0.62 | 0.94 | 21 | empty |
| 3 | 245 | 0.60 | 0.80 | 42 | empty |
| 4 | 117 | 0.54 | 0.83 | 23 | empty |
| 5 | 196 | 0.51 | 0.77 | 39 | empty |
Interfaces
8 interfaces between chains.
- B–G · 2786 Ų buried · 23 hydrogen bonds · protein-protein
- H–L · 1989 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 908 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 471 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 409 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 glycan, 18 disulfide (N-glycosylation, disulfide).
Compared structures
- 6CK9 · Crystal Structure of HIV-1 ConC_Base0 Prefusion Env Trimer in Complex with Human Antibody… · 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 6CK9 · PDBe 6CK9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.