MolNFT v1 · #157283 · protein
Crystal structure of HIV-1 BG505 SOSIP.664 prefusion env trimer bound to small molecule HIV-1 entry inhibitor bms-814508 in complex with human antibodies 3H109L and 35O22 at 3.2 ångström
6MU6 · Envelope glycoprotein GP160: “Crystal structure of HIV-1 BG505 SOSIP.664 prefusion env trimer bound to small molecule HIV-1 entry inhibitor…”. X-ray diffraction, 4 ligands (JYV, NAG, MAN), 20 pockets (best druggability 0.81). MolNFT…
- PDB
- 6MU6
- Type
- protein
- Length
- 1,240 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; 35O22 scfv heavy chain portion; 35O22 scfv light chain…
- UniProt
- Q2N0S6
- Ligands
- JYV, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 13% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Envelope glycoprotein GP160 | protein | 128 | 52% helix, 7% strand | Q2N0S6 |
| D | 35O22 scfv heavy chain portion | protein | 128 | 5% helix, 45% strand | — |
| E | 35O22 scfv light chain portion | protein | 105 | 3% helix, 39% strand | — |
| G | Envelope glycoprotein GP160 | protein | 442 | 13% helix, 43% strand | Q2N0S6 |
| H | 3H109L Fab heavy chain | protein | 226 | 7% helix, 54% strand | — |
| L | 3H109L Fab light chain | protein | 211 | 6% helix, 46% strand | — |
Ligands and binding sites
- JYV · (2R)-{1-[{7-[2-({[3-(dimethylamino)propyl](methyl) amino}methyl)-1,3-thiazol-4-yl]-4-methoxy-1H-pyrrolo[2,3-c]pyridin-3-yl}(oxo)acetyl]piperidin-4-yl}(phenyl)acetonitrile · ligand · chains G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains B, D, G, H
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains 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
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.81 | 0.91 | 38 | NAG, JYV |
| 2 | 83 | 0.71 | 0.95 | 25 | empty |
| 3 | 57 | 0.66 | 0.95 | 25 | empty |
| 4 | 207 | 0.56 | 0.79 | 24 | empty |
| 5 | 246 | 0.53 | 0.76 | 41 | empty |
Interfaces
8 interfaces between chains.
- B–G · 2699 Ų buried · 30 hydrogen bonds · protein-protein
- H–L · 1919 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 887 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 386 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 361 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide, 18 glycan (disulfide, N-glycosylation).
Compared structures
- 6MU6 · Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule… · the same entry in another collection · chain B against B, 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 6MU6 · PDBe 6MU6 · UniProt Q2N0S6
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