Research workbench
Crystal structure of a 3B3 variant, a broadly neutralizing HIV-1 scfv antibody
Analyse Crystal structure of a 3B3 variant, a broadly neutralizing HIV-1 scfv antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JUY
- Type
- protein
- Length
- 1,411 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3B3 single chain variant HIV-1 antibody
- Pockets
- 19 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 3B3 single chain variant HIV-1 antibody | protein | 240 | 4% helix, 46% strand | — |
| A | 3B3 single chain variant HIV-1 antibody | protein | 233 | 4% helix, 44% strand | — |
| C | 3B3 single chain variant HIV-1 antibody | protein | 236 | 4% helix, 46% strand | — |
| E, F, D | 3B3 single chain variant HIV-1 antibody | protein | 234 | 4% helix, 46% strand | — |
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.66 | 0.77 | 51 | empty |
| 2 | 387 | 0.63 | 0.78 | 47 | empty |
| 3 | 576 | 0.61 | 0.74 | 66 | empty |
| 4 | 290 | 0.60 | 0.78 | 53 | empty |
| 5 | 144 | 0.56 | 0.82 | 26 | empty |
Interfaces
9 interfaces between chains.
- B–A · 667 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 594 Ų buried · 10 hydrogen bonds · protein-protein
- F–D · 563 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 559 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 505 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3JUY · Crystal Structure of a 3B3 Variant, a Broadly Neutralizing HIV-1 scFv Antibody · 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 3JUY · PDBe 3JUY
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