Research workbench
Fab structure of HIV GP120 specific mab 1E12
Analyse Fab structure of HIV GP120 specific mab 1E12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UBZ
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-HIV1 GP120 mab 1E12 Fab heavy chain; Anti-HIV1 GP120 mab 1E12 Fab light chain
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Anti-HIV1 GP120 mab 1E12 Fab heavy chain | protein | 222 | 8% helix, 50% strand | — |
| L | Anti-HIV1 GP120 mab 1E12 Fab light chain | protein | 213 | 6% helix, 46% strand | — |
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 | 374 | 0.56 | 0.74 | 40 | empty |
| 2 | 84 | 0.36 | 0.76 | 20 | empty |
| 3 | 64 | 0.28 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- H–L · 1708 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5UBZ · Fab structure of HIV gp120 specific mAb 1E12 · 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 5UBZ · PDBe 5UBZ
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