Research workbench
Cryo-EM structure of CONSOSL.UFO.664 (cons) in complex with bnab PGT122
Analyse Cryo-EM structure of CONSOSL.UFO.664 (cons) in complex with bnab PGT122 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LX2
- Type
- protein
- Length
- 2,322 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Env glycoprotein GP160; PGT122 Fab light chain; PGT122 Fab heavy chain
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 18% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Env glycoprotein GP160 | protein | 534 | 23% helix, 36% strand | — |
| L, M, O | PGT122 Fab light chain | protein | 109 | 3% helix, 45% strand | — |
| H, N, P | PGT122 Fab heavy chain | protein | 131 | 9% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 99 copies · chains A, B, H, L, C, N, M, P, O
- MAN · alpha-D-mannopyranose · sugar · 36 copies · chains A, L, H, B, M, N, C, O, P
- BMA · beta-D-mannopyranose · sugar · 9 copies · chains H, N, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.82 | 0.89 | 49 | empty |
| 2 | 289 | 0.69 | 0.84 | 51 | NAG |
| 3 | 302 | 0.68 | 0.82 | 53 | NAG |
| 4 | 251 | 0.67 | 0.83 | 46 | NAG |
| 5 | 64 | 0.66 | 0.94 | 25 | empty |
Interfaces
12 interfaces between chains.
- B–C · 1159 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1153 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1149 Ų buried · 8 hydrogen bonds · protein-protein
- M–N · 1110 Ų buried · 10 hydrogen bonds · protein-protein
- L–H · 1110 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 57 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 7LX2 · Cryo-EM structure of ConSOSL.UFO.664 (ConS) in complex with bNAb PGT122 · the same entry in another collection · chain N against N, 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 7LX2 · PDBe 7LX2
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