Research workbench
Anti-HIV-1 Fab Fab 2G12 + MAN4 re-refinement
Analyse Anti-HIV-1 Fab Fab 2G12 + MAN4 re-refinement in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MSY
- Type
- protein
- Length
- 423 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 2G12, light chain; Fab 2G12, heavy chain
- UniProt
- P0DOX7, P0DOX5
- Ligands
- MAN, UNX
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab 2G12, light chain | protein | 210 | 6% helix, 53% strand | P0DOX7 |
| H | Fab 2G12, heavy chain | protein | 213 | 7% helix, 54% strand | P0DOX5 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains L, H
- UNX · Unknown atom or ion · ion · 4 copies · chains L, H
- ACT · Acetate ion · additive · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.55 | 0.76 | 37 | empty |
| 2 | 116 | 0.38 | 0.74 | 27 | empty |
| 3 | 112 | 0.35 | 0.73 | 25 | empty |
Interfaces
1 interface between chains.
- L–H · 980 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 P0DOX7
- Every structure of UniProt P0DOX5
- Elsewhere: RCSB PDB 6MSY · PDBe 6MSY · UniProt P0DOX7 · UniProt P0DOX5
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