Research workbench
Cryo-EM structure of edc-crosslinked conm SOSIP.V7 (conm-edc) in complex with bnab PGT122
Analyse Cryo-EM structure of edc-crosslinked conm SOSIP.V7 (conm-edc) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LXN
- Type
- protein
- Length
- 2,373 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 env glycoprotein GP120; HIV-1 env glycoprotein GP41; PGT122 Fab heavy chain; PGT122…
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 19% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | HIV-1 env glycoprotein GP120 | protein | 434 | 13% helix, 42% strand | — |
| B, D, F | HIV-1 env glycoprotein GP41 | protein | 118 | 62% helix, 8% strand | — |
| H, I, J | PGT122 Fab heavy chain | protein | 131 | 11% helix, 54% strand | — |
| L, M, N | PGT122 Fab light chain | protein | 108 | 3% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 93 copies · chains A, H, L, B, C, M, I, D, E, J, N, F
- MAN · alpha-D-mannopyranose · sugar · 48 copies · chains H, A, L, I, C, M, J, E, N
- BMA · beta-D-mannopyranose · sugar · 18 copies · chains H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 811 | 0.82 | 0.85 | 103 | empty |
| 2 | 398 | 0.74 | 0.84 | 59 | NAG |
| 3 | 339 | 0.69 | 0.82 | 61 | NAG |
| 4 | 339 | 0.67 | 0.81 | 59 | NAG |
| 5 | 189 | 0.62 | 0.83 | 47 | empty |
Interfaces
21 interfaces between chains.
- A–B · 2488 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 2477 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2428 Ų buried · 21 hydrogen bonds · protein-protein
- H–L · 1155 Ų buried · 10 hydrogen bonds · protein-protein
- I–M · 1147 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 7LXN · Cryo-EM structure of EDC-crosslinked ConM SOSIP.v7 (ConM-EDC) in complex with bNAb PGT122 · 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
- Elsewhere: RCSB PDB 7LXN · PDBe 7LXN
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