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Isolation and structure of an antibody that fully neutralizes isolate SIVMAC239 reveals functional similarity of SIV and HIV glycan shields
Analyse Isolation and structure of an antibody that fully neutralizes isolate SIVMAC239… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TYB
- Type
- protein
- Length
- 954 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; T-cell surface glycoprotein CD4; Neutralizing antibody…
- UniProt
- E7CWP5, F6XGD3
- Ligands
- MAN, NAG, BMA
- Pockets
- 9 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP160 | protein | 345 | 17% helix, 38% strand | E7CWP5 |
| C | T-cell surface glycoprotein CD4 | protein | 169 | 7% helix, 50% strand | F6XGD3 |
| H | Neutralizing antibody ITS90.03 Fab heavy chain | protein | 227 | 8% helix, 49% strand | — |
| L | Neutralizing antibody ITS90.03 Fab light chain | protein | 213 | 7% helix, 50% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 24 copies · chains H, G, L, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains G, H, C, L
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains H, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.65 | 0.85 | 30 | NAG |
| 2 | 327 | 0.64 | 0.80 | 47 | NAG |
| 3 | 166 | 0.62 | 0.84 | 24 | empty |
| 4 | 391 | 0.58 | 0.75 | 51 | empty |
| 5 | 155 | 0.44 | 0.75 | 26 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1989 Ų buried · 19 hydrogen bonds · protein-protein
- G–C · 1084 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 772 Ų buried · 12 hydrogen bonds · protein-protein
- G–L · 269 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 6TYB · Isolation and Structure of an Antibody that Fully Neutralizes Isolate SIVmac239 Reveals… · the same entry in another collection · chain G against G, 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 E7CWP5
- Every structure of UniProt F6XGD3
- Elsewhere: RCSB PDB 6TYB · PDBe 6TYB · UniProt E7CWP5 · UniProt F6XGD3
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