Research workbench
Crystal structure of the anti-CD4 adnectin 6940_B01 as a complex with the extracellular domains of CD4 and ibalizumab Fab
Analyse Crystal structure of the anti-CD4 adnectin 6940_B01 as a complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T0R
- Type
- protein
- Length
- 1,773 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ibalizumab light chain; Ibalizumab heavy chain; T-cell surface glycoprotein CD4; Adnectin…
- UniProt
- P01730
- Ligands
- NAG, SO4
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 8 distinct chains · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Ibalizumab light chain | protein | 216 | 7% helix, 51% strand | — |
| H | Ibalizumab heavy chain | protein | 221 | 5% helix, 53% strand | — |
| A | T-cell surface glycoprotein CD4 | protein | 355 | 2% helix, 54% strand | P01730 |
| B | Ibalizumab light chain | protein | 215 | 7% helix, 51% strand | — |
| C | Ibalizumab heavy chain | protein | 222 | 3% helix, 48% strand | — |
| D | T-cell surface glycoprotein CD4 | protein | 357 | 2% helix, 50% strand | P01730 |
| G | Adnectin 6940_B01 | protein | 93 | 3% helix, 55% strand | — |
| I | Adnectin 6940_B01 | protein | 94 | 3% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, D
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.67 | 0.93 | 22 | empty |
| 2 | 100 | 0.65 | 0.90 | 22 | empty |
| 3 | 380 | 0.64 | 0.79 | 64 | empty |
| 4 | 659 | 0.63 | 0.74 | 70 | empty |
| 5 | 327 | 0.56 | 0.76 | 46 | empty |
Interfaces
10 interfaces between chains.
- L–H · 1890 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1589 Ų buried · 7 hydrogen bonds · protein-protein
- A–G · 1038 Ų buried · 14 hydrogen bonds · protein-protein
- D–I · 996 Ų buried · 13 hydrogen bonds · protein-protein
- H–A · 723 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7T0R · Crystal structure of the anti-CD4 adnectin 6940_B01 as a complex with the extracellular… · the same entry in another collection · chain I against I, 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 A against A, TM-score 0.55
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 7T0R · PDBe 7T0R · UniProt P01730
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