Research workbench
Crystal structure of rabbit anti-HIV-1 GP120 V3 Fab 10A3 in complex with V3 peptide conb
Analyse Crystal structure of rabbit anti-HIV-1 GP120 V3 Fab 10A3 in complex with V3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V6M
- Type
- protein
- Length
- 445 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of Fab fragment of rabbit anti-HIV1 GP120 V3 mab 10A3; Heavy chain of Fab…
- Ligands
- CA
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Light chain of Fab fragment of rabbit anti-HIV1 GP120 V3 mab 10A3 | protein | 219 | 5% helix, 51% strand | — |
| H | Heavy chain of Fab fragment of rabbit anti-HIV1 GP120 V3 mab 10A3 | protein | 213 | 7% helix, 53% strand | — |
| P | Envelope glycoprotein GP120 V3 peptide of con B sequence | protein | 13 | 0% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.62 | 0.75 | 54 | empty |
| 2 | 55 | 0.52 | 0.88 | 19 | empty |
| 3 | 167 | 0.46 | 0.75 | 24 | empty |
| 4 | 80 | 0.38 | 0.77 | 17 | empty |
| 5 | 60 | 0.27 | 0.73 | 13 | CA |
Interfaces
3 interfaces between chains.
- L–H · 1569 Ų buried · 11 hydrogen bonds · protein-protein
- L–P · 540 Ų buried · 5 hydrogen bonds · protein-protein
- H–P · 393 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5V6M · Crystal Structure of Rabbit Anti-HIV-1 gp120 V3 Fab 10A3 in complex with V3 peptide ConB · 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 5V6M · PDBe 5V6M
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