Research workbench
Vaccine-elicited nhp fp-targeting HIV neutralizing antibody dfph-A.15 in complex with HIV fusion peptide (residue 512-519)
Analyse Vaccine-elicited nhp fp-targeting HIV neutralizing antibody dfph-A.15 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MQE
- Type
- protein
- Length
- 888 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DFPHA.15 antibody Fab light chain; DFPHA.15 antibody Fab heavy chain; HIV fusion peptide
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, L | DFPHA.15 antibody Fab light chain | protein | 212 | 7% helix, 51% strand | — |
| A, H | DFPHA.15 antibody Fab heavy chain | protein | 224 | 7% helix, 50% strand | — |
| C, D | HIV fusion peptide | protein | 8 | 0% helix, 38% strand | — |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 729 | 0.75 | 0.80 | 80 | empty |
| 2 | 262 | 0.61 | 0.80 | 38 | empty |
| 3 | 163 | 0.61 | 0.84 | 36 | empty |
| 4 | 74 | 0.60 | 0.90 | 26 | empty |
| 5 | 164 | 0.54 | 0.80 | 37 | empty |
Interfaces
11 interfaces between chains.
- B–A · 1739 Ų buried · 13 hydrogen bonds · protein-protein
- H–L · 1667 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 592 Ų buried · 13 hydrogen bonds · protein-protein
- H–C · 585 Ų buried · 12 hydrogen bonds · protein-protein
- B–L · 584 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6MQE · Vaccine-elicited NHP FP-targeting HIV neutralizing antibody DFPH-a.15 in complex with HIV… · the same entry in another collection · chain B against B, 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 6MQE · PDBe 6MQE
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