Research workbench
Structure of CD4 mimetic bnm-III-170 in complex with BG505 SOSIP.664 HIV-1 env trimer and 17B Fab
Analyse Structure of CD4 mimetic bnm-III-170 in complex with BG505 SOSIP.664 HIV-1 env… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LO6
- Type
- protein
- Length
- 2,198 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein BG505 SOSIP.664 GP120; HIV-1 envelope glycoprotein BG505 SOSIP.664…
- UniProt
- Q2N0S6
- Ligands
- 5VG, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 8 distinct chains · 21% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein BG505 SOSIP.664 GP120 | protein | 363 | 13% helix, 28% strand | Q2N0S6 |
| B | HIV-1 envelope glycoprotein BG505 SOSIP.664 GP41 | protein | 132 | 58% helix, 5% strand | Q2N0S6 |
| C | Envelope glycoprotein BG505 SOSIP.664 GP120 | protein | 364 | 13% helix, 29% strand | Q2N0S6 |
| D | HIV-1 envelope glycoprotein BG505 SOSIP.664 GP41 | protein | 134 | 60% helix, 1% strand | Q2N0S6 |
| E | Envelope glycoprotein BG505 SOSIP.664 GP120 | protein | 365 | 10% helix, 27% strand | Q2N0S6 |
| F | HIV-1 envelope glycoprotein BG505 SOSIP.664 GP41 | protein | 120 | 58% helix, 5% strand | Q2N0S6 |
| G, I, K | 17B Fab light chain | protein | 111 | 3% helix, 43% strand | — |
| H, J, L | 17B Fab heavy chain | protein | 129 | 2% helix, 47% strand | — |
Ligands and binding sites
- 5VG · ~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-5-(methylaminomethyl)-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide · ligand · 3 copies · chains A, C, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 47 copies · chains A, C, E, D, F
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains A, C, E
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.80 | 0.83 | 90 | empty |
| 2 | 464 | 0.76 | 0.84 | 58 | empty |
| 3 | 197 | 0.70 | 0.87 | 34 | 5VG |
| 4 | 128 | 0.68 | 0.89 | 24 | 5VG |
| 5 | 140 | 0.66 | 0.88 | 25 | 5VG |
Interfaces
21 interfaces between chains.
- C–D · 2483 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 2405 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 2296 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1032 Ų buried · 3 hydrogen bonds · protein-protein
- I–J · 874 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 glycan, 37 disulfide, 2 covalent (disulfide, N-glycosylation, covalent ligand, glycosylation).
Compared structures
- 7LO6 · Structure of CD4 mimetic BNM-III-170 in complex with BG505 SOSIP.664 HIV-1 Env trimer and… · 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
- Every structure of UniProt Q2N0S6
- Elsewhere: RCSB PDB 7LO6 · PDBe 7LO6 · UniProt Q2N0S6
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