Research workbench
Anti-HIV-1 Fab 2G12 + MAN8 re-refinement
Analyse Anti-HIV-1 Fab 2G12 + MAN8 re-refinement in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MNF
- Type
- protein
- Length
- 874 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 2G12, light chain; Fab 2G12, heavy chain
- Ligands
- MAN, BMA
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, K | Fab 2G12, light chain | protein | 213 | 6% helix, 53% strand | — |
| H, M | Fab 2G12, heavy chain | protein | 224 | 7% helix, 50% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains K, M
- BMA · beta-D-mannopyranose · sugar · chains M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.75 | 0.78 | 100 | empty |
| 2 | 377 | 0.62 | 0.78 | 48 | empty |
| 3 | 272 | 0.55 | 0.76 | 38 | empty |
| 4 | 225 | 0.52 | 0.76 | 34 | empty |
| 5 | 134 | 0.51 | 0.80 | 33 | empty |
Interfaces
6 interfaces between chains.
- K–M · 999 Ų buried · 12 hydrogen bonds · protein-protein
- H–M · 965 Ų buried · 13 hydrogen bonds · protein-protein
- L–H · 963 Ų buried · 11 hydrogen bonds · protein-protein
- L–M · 958 Ų buried · 7 hydrogen bonds · protein-protein
- H–K · 890 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6MNF · Anti-HIV-1 Fab 2G12 + Man8 re-refinement · the same entry in another collection · chain L against L, 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 6MNF · PDBe 6MNF
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