Research workbench
PGT145 Fab in complex with full length AMC011 HIV-1 env
Analyse PGT145 Fab in complex with full length AMC011 HIV-1 env in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NIJ
- Type
- protein
- Length
- 2,002 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PGT145 Fab heavy chain; PGT145 Fab light chain; AMC011 glycoprotein 120; AMC011…
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 8 distinct chains · 23% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | PGT145 Fab heavy chain | protein | 140 | 7% helix, 46% strand | — |
| L | PGT145 Fab light chain | protein | 112 | 3% helix, 43% strand | — |
| A | AMC011 glycoprotein 120 | protein | 449 | 15% helix, 36% strand | — |
| B | AMC011 glycoprotein 41 | protein | 140 | 59% helix, 2% strand | — |
| C | AMC011 glycoprotein 120 | protein | 445 | 14% helix, 35% strand | — |
| D | AMC011 glycoprotein 41 | protein | 133 | 65% helix, 5% strand | — |
| E | AMC011 glycoprotein 120 | protein | 444 | 13% helix, 33% strand | — |
| F | AMC011 glycoprotein 41 | protein | 139 | 58% helix, 1% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains H, A, E, C
- BMA · beta-D-mannopyranose · sugar · chains L
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 | 1188 | 0.87 | 0.88 | 156 | empty |
| 2 | 717 | 0.86 | 0.89 | 71 | empty |
| 3 | 595 | 0.84 | 0.89 | 113 | empty |
| 4 | 103 | 0.78 | 0.97 | 29 | empty |
| 5 | 385 | 0.77 | 0.87 | 58 | empty |
Interfaces
19 interfaces between chains.
- C–F · 2895 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2799 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 2422 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 1222 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 1184 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 6NIJ · PGT145 Fab in complex with full length AMC011 HIV-1 Env · the same entry in another collection · chain H against H, 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
- Elsewhere: RCSB PDB 6NIJ · PDBe 6NIJ
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