MolNFT v1 · #152343 · protein
Crystal structure of HIV-1 env conm SOSIP.V7 in complex with bnab PGT124 and 35O22
6IEQ · Envelope glycoprotein GP160: “Crystal structure of HIV-1 env conm SOSIP.V7 in complex with bnab PGT124 and 35O22”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.70). MolNFT v1 #152343 on GenesisL1: 3D…
- PDB
- 6IEQ
- Type
- protein
- Length
- 1,453 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; PGT124 Fab light chain; PGT124 Fab heavy chain; 35O22 Fab…
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP160 | protein | 439 | 12% helix, 38% strand | — |
| B | Envelope glycoprotein GP160 | protein | 131 | 60% helix, 5% strand | — |
| L | PGT124 Fab light chain | protein | 210 | 7% helix, 45% strand | — |
| H | PGT124 Fab heavy chain | protein | 231 | 1% helix, 51% strand | — |
| D | 35O22 Fab heavy chain | protein | 229 | 4% helix, 53% strand | — |
| E | 35O22 Fab light chain | protein | 213 | 4% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains G, B, D, H
- MAN · alpha-D-mannopyranose · sugar · 19 copies · chains D, E, G, L, H
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains D, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.70 | 0.90 | 26 | empty |
| 2 | 361 | 0.67 | 0.81 | 61 | NAG |
| 3 | 154 | 0.58 | 0.83 | 27 | empty |
| 4 | 197 | 0.54 | 0.78 | 22 | empty |
| 5 | 92 | 0.50 | 0.82 | 23 | empty |
Interfaces
8 interfaces between chains.
- G–B · 2773 Ų buried · 22 hydrogen bonds · protein-protein
- L–H · 2047 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1700 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 404 Ų buried · 8 hydrogen bonds · protein-protein
- G–D · 382 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6IEQ · Crystal Structure of HIV-1 Env ConM SOSIP.v7 in Complex with bNAb PGT124 and 35O22 · the same entry in another collection · chain G against G, 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 6IEQ · PDBe 6IEQ
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