Research workbench
Asymmetrically open conformational state (class II) of HIV-1 env trimer BG505 SOSIP.664 in complex with SCD4 and E51 Fab
Analyse Asymmetrically open conformational state (class II) of HIV-1 env trimer BG505… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U0N
- Type
- protein
- Length
- 2,489 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120; T-cell surface glycoprotein CD4; E51 Fab heavy chain; E51…
- UniProt
- Q2N0S6, P01730
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · 9 distinct chains · 15% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein GP120 | protein | 367 | 9% helix, 30% strand | Q2N0S6 |
| B | Envelope glycoprotein GP120 | protein | 364 | 9% helix, 31% strand | Q2N0S6 |
| C | Envelope glycoprotein GP120 | protein | 363 | 7% helix, 29% strand | Q2N0S6 |
| D, E, F | T-cell surface glycoprotein CD4 | protein | 97 | 6% helix, 34% strand | P01730 |
| H, I, P | E51 Fab heavy chain | protein | 132 | 8% helix, 42% strand | — |
| J, L, Q | E51 Fab light chain | protein | 110 | 0% helix, 43% strand | — |
| X | Envelope glycoprotein GP41 | protein | 129 | 40% helix, 5% strand | Q2N0S6 |
| Y | Envelope glycoprotein GP41 | protein | 125 | 50% helix, 1% strand | Q2N0S6 |
| Z | Envelope glycoprotein GP41 | protein | 124 | 48% helix, 7% strand | Q2N0S6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 34 copies · chains A, D, H, B, C, X, I, P, Z
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 667 | 0.74 | 0.80 | 81 | empty |
| 2 | 333 | 0.72 | 0.84 | 52 | empty |
| 3 | 71 | 0.72 | 0.96 | 25 | empty |
| 4 | 66 | 0.71 | 0.97 | 24 | empty |
| 5 | 451 | 0.71 | 0.81 | 71 | empty |
Interfaces
20 interfaces between chains.
- A–X · 2504 Ų buried · 16 hydrogen bonds · protein-protein
- C–Z · 2103 Ų buried · 17 hydrogen bonds · protein-protein
- B–Y · 2074 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 1132 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 1115 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 disulfide, 29 glycan, 6 modified (disulfide, N-glycosylation, sulfation).
Compared structures
- 6U0N · Asymmetrically open conformational state (Class II) of HIV-1 Env trimer BG505 SOSIP.664… · the same entry in another collection · chain Z against Z, 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
- Every structure of UniProt P01730
- Elsewhere: RCSB PDB 6U0N · PDBe 6U0N · UniProt Q2N0S6 · UniProt P01730
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