Research workbench
HIV-1 YU2 GP120 envelope glycoprotein complexed with CD4 and induced neutralizing antibody 17B
Analyse HIV-1 YU2 GP120 envelope glycoprotein complexed with CD4 and induced… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RZK
- Type
- protein
- Length
- 930 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
- P01730
- Ligands
- NAG
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP120 | protein | 306 | 15% helix, 38% strand | — |
| C | T-cell surface glycoprotein CD4 | protein | 181 | 6% helix, 41% strand | P01730 |
| L | Antibody 17B, light chain | protein | 214 | 4% helix, 46% strand | — |
| H | Antibody 17B, heavy chain | protein | 229 | 8% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 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 | 0.71 | 0.98 | 23 | empty |
| 2 | 469 | 0.61 | 0.75 | 50 | empty |
| 3 | 325 | 0.59 | 0.78 | 43 | empty |
| 4 | 124 | 0.55 | 0.82 | 25 | NAG |
| 5 | 88 | 0.55 | 0.86 | 19 | empty |
Interfaces
4 interfaces between chains.
- L–H · 1889 Ų buried · 12 hydrogen bonds · protein-protein
- G–C · 1176 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 543 Ų buried · 8 hydrogen bonds · protein-protein
- G–L · 138 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 glycan, 13 disulfide (N-glycosylation, disulfide).
Compared structures
- 1RZK · HIV-1 YU2 GP120 envelope glycoprotein complexed with CD4 and induced neutralizing… · 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 P01730
- Elsewhere: RCSB PDB 1RZK · PDBe 1RZK · UniProt P01730
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