Research workbench
Cryo-EM structure of DH898.1 Fab-dimer bound near the CD4 binding site of HIV-1 env CH848 sosip trimer
Analyse Cryo-EM structure of DH898.1 Fab-dimer bound near the CD4 binding site of HIV-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LUA
- Type
- protein
- Length
- 2,650 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CH848 sosip GP120; Env polyprotein; DH898.1 light chain; DH898.1 heavy chain
- UniProt
- A0A1W6IPB2, A0A6H1VEB8
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 17% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a, c, e | CH848 sosip GP120 | protein | 466 | 15% helix, 37% strand | A0A1W6IPB2 |
| b, d, f | Env polyprotein | protein | 126 | 59% helix, 6% strand | A0A6H1VEB8 |
| g, j | DH898.1 light chain | protein | 218 | 6% helix, 50% strand | — |
| h, i | DH898.1 heavy chain | protein | 219 | 8% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 97 copies · chains e, a, c, b, d, f
- BMA · beta-D-mannopyranose · sugar · 31 copies
- MAN · alpha-D-mannopyranose · sugar · 11 copies · chains g, h, i, j, a, c
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.80 | 0.91 | 49 | empty |
| 2 | 972 | 0.77 | 0.79 | 99 | empty |
| 3 | 665 | 0.73 | 0.80 | 86 | empty |
| 4 | 239 | 0.70 | 0.86 | 53 | NAG |
| 5 | 403 | 0.70 | 0.82 | 59 | NAG |
Interfaces
15 interfaces between chains.
- e–f · 2616 Ų buried · 32 hydrogen bonds · protein-protein
- c–d · 2605 Ų buried · 35 hydrogen bonds · protein-protein
- a–b · 2583 Ų buried · 34 hydrogen bonds · protein-protein
- i–j · 2079 Ų buried · 21 hydrogen bonds · protein-protein
- g–h · 1951 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 53 glycan, 44 disulfide (N-glycosylation, disulfide, O-glycosylation).
Compared structures
- 7LUA · Cryo-EM structure of DH898.1 Fab-dimer bound near the CD4 binding site of HIV-1 Env CH848… · 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 A0A1W6IPB2
- Every structure of UniProt A0A6H1VEB8
- Elsewhere: RCSB PDB 7LUA · PDBe 7LUA · UniProt A0A1W6IPB2 · UniProt A0A6H1VEB8
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