Research workbench
Cryo-EM model of B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen binding variable domain of 17B
Analyse Cryo-EM model of B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VN3
- Type
- protein
- Length
- 2,814 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 17B Fab light chain; Envelope glycoprotein GP160; T-cell surface glycoprotein CD4; 17B…
- UniProt
- B3UEZ6, B3UES2, P01730
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 5 distinct chains · 15% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, N, O | 17B Fab light chain | protein | 110 | 0% helix, 43% strand | — |
| A, B, D | Envelope glycoprotein GP160 | protein | 136 | 58% helix, 1% strand | B3UEZ6 |
| G, I, J | Envelope glycoprotein GP160 | protein | 389 | 13% helix, 30% strand | B3UES2 |
| C, E, F | T-cell surface glycoprotein CD4 | protein | 176 | 3% helix, 33% strand | P01730 |
| H, K, M | 17B Fab heavy chain | protein | 127 | 2% helix, 35% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 90 copies · chains G, C, I, E, J, F, A, B, D
- BMA · beta-D-mannopyranose · sugar · 21 copies · chains G, I
- MAN · alpha-D-mannopyranose · sugar · 18 copies · chains G, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 699 | 0.75 | 0.81 | 70 | empty |
| 2 | 65 | 0.74 | 0.99 | 20 | empty |
| 3 | 798 | 0.73 | 0.78 | 59 | empty |
| 4 | 579 | 0.73 | 0.80 | 55 | empty |
| 5 | 60 | 0.73 | 0.98 | 19 | empty |
Interfaces
24 interfaces between chains.
- A–G · 2362 Ų buried · 21 hydrogen bonds · protein-protein
- B–I · 2362 Ų buried · 21 hydrogen bonds · protein-protein
- D–J · 2350 Ų buried · 20 hydrogen bonds · protein-protein
- J–F · 1243 Ų buried · 16 hydrogen bonds · protein-protein
- I–E · 1225 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 64 glycan, 42 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 5VN3 · Cryo-EM model of B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen… · the same entry in another collection · chain M against M, TM-score 1.00
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 5VN3 · PDBe 5VN3 · UniProt B3UEZ6 · UniProt B3UES2 · UniProt P01730
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