Research workbench
Crystal structure of anti-HIV-1 Fab 537-10D in complex with V3 peptide MN
Analyse Crystal structure of anti-HIV-1 Fab 537-10D in complex with V3 peptide MN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GHE
- Type
- protein
- Length
- 451 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Fab 537-10D, light chain; Fab 537-10D, heavy chain; Envelope glycoprotein
- UniProt
- P88403
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · resolution 2.4 · 3 distinct chains · 8% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab 537-10D, light chain | protein | 214 | 6% helix, 49% strand | — |
| H | Fab 537-10D, heavy chain | protein | 222 | 10% helix, 57% strand | — |
| P | Envelope glycoprotein | protein | 15 | 0% helix, 73% strand | P88403 |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.34 | 0.73 | 21 | empty |
| 2 | 64 | 0.29 | 0.73 | 13 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1690 Ų buried · 16 hydrogen bonds · protein-protein
- H–P · 596 Ų buried · 17 hydrogen bonds · protein-protein
- L–P · 309 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3GHE · Crystal structure of anti-HIV-1 Fab 537-10D in complex with V3 peptide mn · 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
- Every structure of UniProt P88403
- Elsewhere: RCSB PDB 3GHE · PDBe 3GHE · UniProt P88403
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