Research workbench
AB1245 Fab in complex with BG505 SOSIP.664 and 8ANC195 Fab
Analyse AB1245 Fab in complex with BG505 SOSIP.664 and 8ANC195 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MXE
- Type
- protein
- Length
- 2,632 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 8ANC195 G52K5 Fab heavy chain; 8ANC195 G52K5 Fab light chain; HIV-1 envelope glycoprotein…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 9 distinct chains · 15% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H, M | 8ANC195 G52K5 Fab heavy chain | protein | 132 | 0% helix, 48% strand | — |
| B, L, O | 8ANC195 G52K5 Fab light chain | protein | 108 | 3% helix, 46% strand | — |
| C | HIV-1 envelope glycoprotein BG505 SOSIP.664 GP41 | protein | 124 | 46% helix, 4% strand | Q2N0S6 |
| D | HIV-1 envelope glycoprotein BG505 SOSIP.664 GP41 | protein | 122 | 43% helix, 5% strand | Q2N0S6 |
| F | HIV-1 envelope glycoprotein BG505 SOSIP.664 GP41 | protein | 99 | 60% helix, 5% strand | Q2N0S6 |
| G, J | Envelope glycoprotein BG505 SOSIP.664 GP120 | protein | 442 | 10% helix, 38% strand | Q2N0S6 |
| P | Envelope glycoprotein BG505 SOSIP.664 GP120 | protein | 438 | 10% helix, 37% strand | Q2N0S6 |
| R | AB1245 Fab heavy chain | protein | 129 | 2% helix, 45% strand | — |
| W | AB1245 Fab light chain | protein | 116 | 0% helix, 41% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 87 copies · chains C, O, M, D, L, B, F, A, G, J, H, P, R
- MAN · alpha-D-mannopyranose · sugar · 30 copies · chains G, H, A, M
- BMA · beta-D-mannopyranose · sugar · 11 copies · chains H, A, J, R, M
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 | 575 | 0.80 | 0.86 | 60 | empty |
| 2 | 1168 | 0.77 | 0.79 | 104 | empty |
| 3 | 301 | 0.71 | 0.84 | 48 | NAG |
| 4 | 379 | 0.70 | 0.82 | 53 | empty |
| 5 | 847 | 0.69 | 0.75 | 89 | empty |
Interfaces
32 interfaces between chains.
- D–G · 2625 Ų buried · 16 hydrogen bonds · protein-protein
- C–P · 2616 Ų buried · 11 hydrogen bonds · protein-protein
- F–J · 2072 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1022 Ų buried · 7 hydrogen bonds · protein-protein
- R–W · 1008 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 glycan, 40 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 7MXE · Ab1245 Fab in complex with BG505 SOSIP.664 and 8ANC195 Fab · the same entry in another collection · chain A against A, 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 7MXE · PDBe 7MXE · UniProt Q2N0S6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.