MolNFT v1 · #46224 · protein
HIV-1 GP120 envelope glycoprotein (I109C, T257S, S334A, S375W, Q428C) complexed with CD4 and antibody 17B
2NY1 · Envelope glycoprotein GP120: “HIV-1 GP120 envelope glycoprotein (I109C, T257S, S334A, S375W, Q428C) complexed with CD4 and antibody 17B”. X-ray diffraction, 3 ligands (NAG, GLC, FRU), 9 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 2NY1
- 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
- Q993A8, P01730, Q6P5S8, Q6N030
- Ligands
- NAG, GLC, FRU
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein GP120 | protein | 305 | 16% helix, 37% strand | Q993A8 |
| B | T-cell surface glycoprotein CD4 | protein | 181 | 8% helix, 52% strand | P01730 |
| C | Antibody 17B, light chain | protein | 214 | 5% helix, 50% strand | Q6P5S8 |
| D | Antibody 17B, heavy chain | protein | 223 | 8% helix, 50% strand | Q6N030 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A
- 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
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.72 | 0.98 | 20 | empty |
| 2 | 92 | 0.63 | 0.89 | 18 | empty |
| 3 | 338 | 0.59 | 0.77 | 38 | empty |
| 4 | 426 | 0.58 | 0.75 | 53 | empty |
| 5 | 92 | 0.52 | 0.83 | 20 | NAG |
Interfaces
4 interfaces between chains.
- C–D · 1754 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1102 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 543 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 143 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
- 2NY1 · HIV-1 gp120 Envelope Glycoprotein (I109C, T257S, S334A, S375W, Q428C) 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 0.98
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 Q993A8
- Every structure of UniProt P01730
- Every structure of UniProt Q6P5S8
- Every structure of UniProt Q6N030
- Elsewhere: RCSB PDB 2NY1 · PDBe 2NY1 · UniProt Q993A8 · UniProt P01730 · UniProt Q6P5S8 · UniProt Q6N030
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