Research workbench
Cryo-EM structure of DH898.1 Fab-dimer from local refinement of the Fab-dimer bound near the CD4 binding site of HIV-1 env CH848 sosip trimer
Analyse Cryo-EM structure of DH898.1 Fab-dimer from local refinement of the Fab-dimer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L6M
- Type
- protein
- Length
- 874 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DH898.1 Fab light chain; DH898.1 Fab heavy chain
- Pockets
- 12 · best druggability 0.76
Structure
electron microscopy · 2 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| g, j | DH898.1 Fab light chain | protein | 218 | 6% helix, 49% strand | — |
| h, i | DH898.1 Fab heavy chain | protein | 219 | 8% helix, 51% strand | — |
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.76 | 0.79 | 96 | empty |
| 2 | 87 | 0.71 | 0.94 | 26 | empty |
| 3 | 106 | 0.66 | 0.90 | 25 | empty |
| 4 | 82 | 0.59 | 0.88 | 25 | empty |
| 5 | 67 | 0.58 | 0.89 | 21 | empty |
Interfaces
3 interfaces between chains.
- i–j · 1746 Ų buried · 7 hydrogen bonds · protein-protein
- g–h · 1695 Ų buried · 14 hydrogen bonds · protein-protein
- h–i · 563 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7L6M · Cryo-EM structure of DH898.1 Fab-dimer from local refinement of the Fab-dimer bound near… · the same entry in another collection · chain g against g, 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 7L6M · PDBe 7L6M
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