MolNFT v1 · #46228 · protein
HIV-1 GP120 envelope glycoprotein (M95W, W96C, I109C, T257S, V275C, S334A, S375W, Q428C, A433M) complexed with CD4 and antibody 17B
2NY5 · Envelope glycoprotein GP120: “HIV-1 GP120 envelope glycoprotein (M95W, W96C, I109C, T257S, V275C, S334A, S375W, Q428C, A433M) complexed…”. X-ray diffraction, 3 ligands (NAG, GLC, FRU), 10 pockets (best druggability 0.70). MolNFT v1…
- PDB
- 2NY5
- Type
- protein
- Length
- 920 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
- Q71057, P01730, Q6P5S8, Q6PJA4
- Ligands
- NAG, GLC, FRU
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP120 | protein | 304 | 17% helix, 38% strand | Q71057 |
| C | T-cell surface glycoprotein CD4 | protein | 181 | 7% helix, 49% strand | P01730 |
| L | Antibody 17B, light chain | protein | 214 | 6% helix, 50% strand | Q6P5S8 |
| H | Antibody 17B, heavy chain | protein | 221 | 10% helix, 52% strand | Q6PJA4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains G
- GLC · alpha-D-glucopyranose · sugar · chains L, H
- FRU · beta-D-fructofuranose · sugar · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.70 | 0.98 | 21 | empty |
| 2 | 209 | 0.65 | 0.84 | 29 | NAG |
| 3 | 64 | 0.64 | 0.93 | 22 | empty |
| 4 | 469 | 0.59 | 0.74 | 59 | empty |
| 5 | 320 | 0.58 | 0.77 | 41 | empty |
Interfaces
4 interfaces between chains.
- L–H · 1758 Ų buried · 11 hydrogen bonds · protein-protein
- G–C · 1110 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 508 Ų buried · 5 hydrogen bonds · protein-protein
- G–L · 144 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 2NY5 · HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T257S, V275C, S334A, S375W, Q428C… · the same entry in another collection · chain G against G, 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 C 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 Q71057
- Every structure of UniProt P01730
- Every structure of UniProt Q6P5S8
- Every structure of UniProt Q6PJA4
- Elsewhere: RCSB PDB 2NY5 · PDBe 2NY5 · UniProt Q71057 · UniProt P01730 · UniProt Q6P5S8 · UniProt Q6PJA4
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