Research workbench
Crystal structure of bovine Fab nc-COW1 in complex with HIV-1 BG505 SOSIP.664, and human fabs 35022 and PGT128
Analyse Crystal structure of bovine Fab nc-COW1 in complex with HIV-1 BG505 SOSIP.664… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OPA
- Type
- protein
- Length
- 1,310 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; Envelope glycoprotein GP41; Fab 35022 heavy chain; Fab 35022…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA
- Pockets
- 14 · best druggability 0.66
Structure
x-ray diffraction · 8 distinct chains · 13% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP160 | protein | 427 | 13% helix, 40% strand | Q2N0S6 |
| B | Envelope glycoprotein GP41 | protein | 129 | 58% helix, 5% strand | Q2N0S6 |
| F | Fab 35022 heavy chain | protein | 130 | 5% helix, 51% strand | — |
| I | Fab 35022 light chain | protein | 110 | 3% helix, 46% strand | — |
| J | Fab PGT128 light chain | protein | 102 | 3% helix, 49% strand | — |
| K | Fab PGT128 heavy chain | protein | 132 | 5% helix, 52% strand | — |
| R | Fab nc-COW1 light chain | protein | 112 | 3% helix, 49% strand | — |
| S | Fab nc-COW1 heavy chain | protein | 168 | 11% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 28 copies · chains G, B, F, K, S, I
- MAN · alpha-D-mannopyranose · sugar · 15 copies · chains F, I, G, K, J, S
- BMA · beta-D-mannopyranose · sugar · 11 copies · chains F, I, S, K, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.66 | 0.82 | 42 | empty |
| 2 | 356 | 0.64 | 0.79 | 37 | empty |
| 3 | 216 | 0.62 | 0.82 | 38 | empty |
| 4 | 117 | 0.56 | 0.83 | 42 | NAG |
| 5 | 79 | 0.49 | 0.83 | 18 | empty |
Interfaces
9 interfaces between chains.
- G–B · 2813 Ų buried · 19 hydrogen bonds · protein-protein
- R–S · 1093 Ų buried · 9 hydrogen bonds · protein-protein
- J–K · 966 Ų buried · 9 hydrogen bonds · protein-protein
- F–I · 830 Ų buried · 6 hydrogen bonds · protein-protein
- G–S · 810 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 6OPA · Crystal structure of bovine Fab NC-Cow1 in complex with HIV-1 BG505 SOSIP.664, and human… · 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 Q2N0S6
- Elsewhere: RCSB PDB 6OPA · PDBe 6OPA · UniProt Q2N0S6
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