Research workbench
Structure of simian immunodeficiency virus envelope spikes bound with CD4 and monoclonal antibody 36D5
Analyse Structure of simian immunodeficiency virus envelope spikes bound with CD4 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JCB
- Type
- protein
- Length
- 1,863 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120; Antibody 36D5 light chain; Antibody 36D5 heavy chain; T-cell…
- UniProt
- P01730
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 10% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | Envelope glycoprotein GP120 | protein | 420 | 14% helix, 31% strand | — |
| B | Antibody 36D5 light chain | protein | 202 | 7% helix, 47% strand | — |
| C | Antibody 36D5 heavy chain | protein | 226 | 9% helix, 52% strand | — |
| D | T-cell surface glycoprotein CD4 | protein | 175 | 7% helix, 46% strand | P01730 |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.82 | 0.83 | 133 | empty |
| 2 | 461 | 0.76 | 0.84 | 74 | empty |
| 3 | 69 | 0.71 | 0.97 | 24 | empty |
| 4 | 355 | 0.71 | 0.83 | 50 | empty |
| 5 | 433 | 0.70 | 0.81 | 76 | empty |
Interfaces
7 interfaces between chains.
- B–C · 1878 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 846 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 256 Ų buried · 0 hydrogen bonds · protein-protein
- D–I · 240 Ų buried · 2 hydrogen bonds · protein-protein
- A–I · 149 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 disulfide, 1 isopeptide (disulfide, isopeptide).
Compared structures
- 3JCB · Structure of Simian Immunodeficiency Virus Envelope Spikes bound with CD4 and Monoclonal… · 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 D 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 3JCB · PDBe 3JCB · UniProt P01730
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