Research workbench
anti-HIV-1 gp120-sCD4 complex antibody CG10 Fab in complex with B41-sCD4
Analyse anti-HIV-1 gp120-sCD4 complex antibody CG10 Fab in complex with B41-sCD4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8D5C
- Type
- protein
- Length
- 2,730 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.9
- Source
- Homo sapiens; Human immunodeficiency virus; Human immunodeficiency virus 1; Mus…
- Molecule
- Envelope glycoprotein gp41; Envelope glycoprotein gp160; T-cell surface glycoprotein CD4…
- UniProt
- B3UEZ6, B3UES2, P01730
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · resolution 3.9 · 7 distinct chains · 13% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, Y, Z | Envelope glycoprotein gp41 | protein | 129 | 60% helix, 1% strand | B3UEZ6 |
| A, B, C | Envelope glycoprotein gp160 | protein | 377 | 12% helix, 31% strand | B3UES2 |
| D, E, F | T-cell surface glycoprotein CD4 | protein | 176 | 6% helix, 24% strand | P01730 |
| H | CG10 Fab heavy chain | protein | 122 | 5% helix, 45% strand | — |
| L, J, Q | CG10 Fab light chain | protein | 113 | 3% helix, 50% strand | — |
| I | CG10 Fab heavy chain | protein | 119 | 3% helix, 40% strand | — |
| P | CG10 Fab heavy chain | protein | 104 | 6% helix, 49% strand | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.84 | 0.85 | 105 | empty |
| 2 | 778 | 0.81 | 0.84 | 87 | empty |
| 3 | 195 | 0.79 | 0.93 | 27 | empty |
| 4 | 131 | 0.79 | 0.96 | 36 | empty |
| 5 | 771 | 0.78 | 0.81 | 67 | empty |
Interfaces
27 interfaces between chains.
- X–A · 2002 Ų buried · 12 hydrogen bonds · protein-protein
- Y–B · 1992 Ų buried · 11 hydrogen bonds · protein-protein
- Z–C · 1941 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 1118 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1079 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide (disulfide).
Compared structures
- P01730 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD4 (P01730) · a predicted model of the same protein · chain F against A, TM-score 0.95
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 B3UEZ6
- Every structure of UniProt B3UES2
- Every structure of UniProt P01730
- Elsewhere: RCSB PDB 8D5C · PDBe 8D5C · UniProt B3UEZ6 · UniProt B3UES2 · UniProt P01730
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