MolNFT v1 · #165526 · protein
Isolation and structure of an antibody that fully neutralizes isolate SIVMAC239 reveals functional similarity of SIV and HIV glycan shields
6TYB · Envelope glycoprotein GP160: “Isolation and structure of an antibody that fully neutralizes isolate SIVMAC239 reveals functional similarity…”. X-ray diffraction, 3 ligands (MAN, NAG, BMA), 9 pockets (best druggability 0.65). MolNFT…
- 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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