Research workbench
Vaccine-elicited nhp fp-targeting neutralizing antibody 0PV-A.01 in complex with fp (residue 512-519)
Analyse Vaccine-elicited nhp fp-targeting neutralizing antibody 0PV-A.01 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MQR
- Type
- protein
- Length
- 448 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody 0PV-A.01 Fab heavy chain; Antibody 0PV-A.01 Fab light chain; HIV fusion peptide…
- Ligands
- CA, SO4
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Antibody 0PV-A.01 Fab heavy chain | protein | 227 | 7% helix, 49% strand | — |
| L | Antibody 0PV-A.01 Fab light chain | protein | 213 | 6% helix, 51% strand | — |
| A | HIV fusion peptide residue 512-519 | protein | 8 | 38% helix, 0% strand | — |
Ligands and binding sites
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 | 529 | 0.61 | 0.74 | 54 | empty |
| 2 | 64 | 0.53 | 0.87 | 18 | empty |
| 3 | 201 | 0.49 | 0.76 | 32 | empty |
| 4 | 92 | 0.34 | 0.74 | 20 | empty |
| 5 | 54 | 0.25 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1639 Ų buried · 15 hydrogen bonds · protein-protein
- H–A · 343 Ų buried · 3 hydrogen bonds · protein-protein
- L–A · 263 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6MQR · Vaccine-elicited NHP FP-targeting neutralizing antibody 0PV-a.01 in complex with FP… · 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 6MQR · PDBe 6MQR
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