MolNFT v1 · #46221 · protein
HIV-1 GP120 envelope GLYCOPROTEIN(S334A) complexed with CD4 and antibody 17B
2NXY · Envelope glycoprotein GP120: “HIV-1 GP120 envelope GLYCOPROTEIN(S334A) complexed with CD4 and antibody 17B”. X-ray diffraction, 1 ligand (NAG), 11 pockets (best druggability 0.70). MolNFT v1 #46221 on GenesisL1: 3D structure…
- PDB
- 2NXY
- Type
- protein
- Length
- 926 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
- Q49DS8, P01730, Q6P5S8, Q6N095
- Ligands
- NAG
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein GP120 | protein | 304 | 17% helix, 38% strand | Q49DS8 |
| 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 | 227 | 8% helix, 51% strand | Q6N095 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B
- HEZ · Hexane-1,6-diol · additive · 3 copies · chains A, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 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 | 0.70 | 0.98 | 17 | TRS |
| 2 | 53 | 0.69 | 0.98 | 19 | empty |
| 3 | 440 | 0.59 | 0.75 | 52 | empty |
| 4 | 317 | 0.57 | 0.77 | 40 | empty |
| 5 | 85 | 0.55 | 0.85 | 22 | NAG |
Interfaces
4 interfaces between chains.
- C–D · 1825 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1148 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 539 Ų buried · 6 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
- 2NXY · HIV-1 gp120 Envelope Glycoprotein(S334A) Complexed with CD4 and Antibody 17b · 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 Q49DS8
- Every structure of UniProt P01730
- Every structure of UniProt Q6P5S8
- Every structure of UniProt Q6N095
- Elsewhere: RCSB PDB 2NXY · PDBe 2NXY · UniProt Q49DS8 · UniProt P01730 · UniProt Q6P5S8 · UniProt Q6N095
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