Research workbench
Fab structure of anti-HIV-1 GP120 mab 1A8
Analyse Fab structure of anti-HIV-1 GP120 mab 1A8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UBY
- Type
- protein
- Length
- 439 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of Fab fragment of anti-HIV1 GP120 mab 1A8; Light chain of Fab fragment of…
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain of Fab fragment of anti-HIV1 GP120 mab 1A8 | protein | 228 | 6% helix, 50% strand | — |
| L | Light chain of Fab fragment of anti-HIV1 GP120 mab 1A8 | protein | 211 | 8% helix, 45% strand | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.66 | 0.76 | 57 | empty |
| 2 | 384 | 0.63 | 0.78 | 54 | empty |
| 3 | 82 | 0.36 | 0.76 | 22 | empty |
| 4 | 75 | 0.34 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- H–L · 1842 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5UBY · Fab structure of anti-HIV-1 gp120 mAb 1A8 · the same entry in another collection · chain H against H, 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 5UBY · PDBe 5UBY
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