Research workbench
HIV-1 GP120 envelope glycoprotein (K231C, T257S, E268C, S334A, S375W) complexed with CD4 and antibody 17B
Analyse HIV-1 GP120 envelope glycoprotein (K231C, T257S, E268C, S334A, S375W) complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NY4
- Type
- protein
- Length
- 923 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
- Q8QDX5, P01730, Q6P5S8, Q6PJA4
- Ligands
- NAG, GLC, FRU
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein GP120 | protein | 306 | 17% helix, 37% strand | Q8QDX5 |
| B | T-cell surface glycoprotein CD4 | protein | 181 | 8% helix, 51% strand | P01730 |
| C | Antibody 17B, light chain | protein | 214 | 6% helix, 50% strand | Q6P5S8 |
| D | Antibody 17B, heavy chain | protein | 222 | 8% helix, 51% strand | Q6PJA4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · chains C, D
- FRU · beta-D-fructofuranose · sugar · chains C, D
- HEZ · Hexane-1,6-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.68 | 0.97 | 20 | empty |
| 2 | 332 | 0.59 | 0.77 | 38 | empty |
| 3 | 422 | 0.58 | 0.75 | 46 | empty |
| 4 | 76 | 0.54 | 0.86 | 22 | empty |
| 5 | 72 | 0.50 | 0.85 | 18 | NAG |
Interfaces
4 interfaces between chains.
- C–D · 1770 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1144 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 529 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 144 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 13 glycan (disulfide, N-glycosylation).
Compared structures
- 2NY4 · HIV-1 gp120 Envelope Glycoprotein (K231C, T257S, E268C, S334A, S375W) Complexed with CD4… · the same entry in another collection · chain A against A, 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 0.97
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 Q8QDX5
- Every structure of UniProt P01730
- Every structure of UniProt Q6P5S8
- Every structure of UniProt Q6PJA4
- Elsewhere: RCSB PDB 2NY4 · PDBe 2NY4 · UniProt Q8QDX5 · UniProt P01730 · UniProt Q6P5S8 · UniProt Q6PJA4
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