Research workbench
HIV-1 GP120 envelope glycoprotein (M95W, W96C, I109C, T123C, T257S, V275C,S334A, S375W, Q428C, G431C) complexed with CD4 and antibody 17B
Analyse HIV-1 GP120 envelope glycoprotein (M95W, W96C, I109C, T123C, T257S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NY6
- Type
- protein
- Length
- 921 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120; T-cell surface glycoprotein CD4; Antibody 17B, light chain…
- UniProt
- Q8Q7Z9, P01730, Q6P5S8, Q6N030
- Ligands
- NAG, GLC, FRU
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein GP120 | protein | 304 | 18% helix, 37% strand | Q8Q7Z9 |
| B | T-cell surface glycoprotein CD4 | protein | 181 | 7% helix, 50% strand | P01730 |
| C | Antibody 17B, light chain | protein | 214 | 6% helix, 50% strand | Q6P5S8 |
| D | Antibody 17B, heavy chain | protein | 222 | 5% helix, 50% strand | Q6N030 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · chains C, D
- FRU · beta-D-fructofuranose · sugar · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.70 | 0.98 | 19 | empty |
| 2 | 218 | 0.64 | 0.83 | 27 | NAG |
| 3 | 344 | 0.60 | 0.77 | 48 | empty |
| 4 | 450 | 0.59 | 0.75 | 50 | empty |
| 5 | 209 | 0.49 | 0.75 | 30 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1746 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1138 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 521 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 142 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 2NY6 · HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T123C, T257S, V275C,S334A, S375W… · the same entry in another collection · chain B against B, TM-score 1.00
- P01730 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD4 (P01730) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q8Q7Z9
- Every structure of UniProt P01730
- Every structure of UniProt Q6P5S8
- Every structure of UniProt Q6N030
- Elsewhere: RCSB PDB 2NY6 · PDBe 2NY6 · UniProt Q8Q7Z9 · UniProt P01730 · UniProt Q6P5S8 · UniProt Q6N030
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