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Crystal structure of HIV-1 jr-fl GP120 core protein containing the third variable region (V3) complexed with CD4 and the X5 antibody
Analyse Crystal structure of HIV-1 jr-fl GP120 core protein containing the third… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B4C
- Type
- protein
- Length
- 962 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein; T-cell surface glycoprotein CD4; Anti-HIV-1 GP120 immunoglobulin…
- UniProt
- P01730
- Ligands
- XYL, NAG, FUC, SO4
- Pockets
- 15 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein | protein | 339 | 12% helix, 36% strand | — |
| C | T-cell surface glycoprotein CD4 | protein | 175 | 7% helix, 46% strand | P01730 |
| L | Anti-HIV-1 GP120 immunoglobulin X5 light chain | protein | 215 | 6% helix, 49% strand | — |
| H | Anti-HIV-1 GP120 immunoglobulin X5 heavy chain | protein | 233 | 8% helix, 47% strand | — |
Ligands and binding sites
- XYL · Xylitol · ligand · 3 copies · chains H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains G
- FUC · alpha-L-fucopyranose · sugar · chains C
- SO4 · Sulfate ion · ion · 5 copies · chains G, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.72 | 0.97 | 25 | empty |
| 2 | 593 | 0.64 | 0.75 | 50 | empty |
| 3 | 612 | 0.63 | 0.74 | 58 | empty |
| 4 | 260 | 0.60 | 0.80 | 27 | empty |
| 5 | 245 | 0.57 | 0.79 | 29 | empty |
Interfaces
5 interfaces between chains.
- L–H · 2022 Ų buried · 10 hydrogen bonds · protein-protein
- G–C · 1251 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 830 Ų buried · 9 hydrogen bonds · protein-protein
- G–L · 114 Ų buried · 1 hydrogen bond · protein-protein
- C–H · 41 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 14 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 2B4C · Crystal structure of HIV-1 JR-FL gp120 core protein containing the third variable region… · 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 2B4C · PDBe 2B4C · UniProt P01730
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