Research workbench
Crystal structure of clade C GP120 in complex with SCD4 and 21C Fab
Analyse Crystal structure of clade C GP120 in complex with SCD4 and 21C Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LQA
- Type
- protein
- Length
- 903 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface glycoprotein CD4; Envelope glycoprotein GP160; Heavy chain of anti HIV Fab…
- UniProt
- P01730, Q1PHM6
- Ligands
- NAG
- Pockets
- 19 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | T-cell surface glycoprotein CD4 | protein | 175 | 2% helix, 45% strand | P01730 |
| G | Envelope glycoprotein GP160 | protein | 290 | 17% helix, 31% strand | Q1PHM6 |
| H | Heavy chain of anti HIV Fab from human 21C antibody | protein | 225 | 5% helix, 47% strand | — |
| L | Light chain of anti HIV Fab from human 21C antibody | protein | 213 | 8% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.78 | 0.91 | 39 | empty |
| 2 | 91 | 0.75 | 0.97 | 25 | empty |
| 3 | 462 | 0.74 | 0.83 | 42 | empty |
| 4 | 364 | 0.59 | 0.77 | 44 | empty |
| 5 | 93 | 0.59 | 0.86 | 22 | NAG |
Interfaces
5 interfaces between chains.
- H–L · 1919 Ų buried · 13 hydrogen bonds · protein-protein
- C–G · 1104 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 687 Ų buried · 13 hydrogen bonds · protein-protein
- C–L · 269 Ų buried · 3 hydrogen bonds · protein-protein
- C–H · 163 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3LQA · Crystal structure of clade C gp120 in complex with sCD4 and 21c Fab · the same entry in another collection · chain C against C, 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 0.96
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
- Every structure of UniProt Q1PHM6
- Elsewhere: RCSB PDB 3LQA · PDBe 3LQA · UniProt P01730 · UniProt Q1PHM6
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