Research workbench
Vaccine-elicited nhp fp-targeting neutralizing antibody A12V163-A.02 in complex with HIV fusion peptide (residue 512-519)
Analyse Vaccine-elicited nhp fp-targeting neutralizing antibody A12V163-A.02 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P60
- Type
- protein
- Length
- 1,750 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody A12V163-A.02 heavy chain; Antibody A12V163-A.02 light chain; HIV fusion peptide…
- Pockets
- 19 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Antibody A12V163-A.02 heavy chain | protein | 221 | 9% helix, 49% strand | — |
| B, D | Antibody A12V163-A.02 light chain | protein | 211 | 7% helix, 51% strand | — |
| E, F, I, L | HIV fusion peptide residue 512-519 | protein | 8 | 0% helix, 0% strand | — |
| G, J | Antibody A12V163-A.02 heavy chain | protein | 215 | 7% helix, 51% strand | — |
| H, K | Antibody A12V163-A.02 light chain | protein | 212 | 7% helix, 51% strand | — |
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.72 | 0.85 | 41 | empty |
| 2 | 574 | 0.60 | 0.73 | 62 | empty |
| 3 | 535 | 0.60 | 0.74 | 53 | empty |
| 4 | 560 | 0.60 | 0.73 | 52 | empty |
| 5 | 468 | 0.58 | 0.74 | 52 | empty |
Interfaces
19 interfaces between chains.
- A–B · 1694 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1678 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 1642 Ų buried · 15 hydrogen bonds · protein-protein
- J–K · 1569 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 420 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6P60 · Vaccine-elicited NHP FP-targeting neutralizing antibody A12V163-a.02 in complex with HIV… · the same entry in another collection · chain A against A, 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 6P60 · PDBe 6P60
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