Research workbench
Fab fragment of HIV vaccine-elicited CD4BS-directed antibody, GE356, from a non-human primate
Analyse Fab fragment of HIV vaccine-elicited CD4BS-directed antibody, GE356, from a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q2Z
- Type
- protein
- Length
- 872 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of Fab fragment of HIV vaccine-elicited CD4BS- directed antibody; Light chain…
- Pockets
- 15 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A | Heavy chain of Fab fragment of HIV vaccine-elicited CD4BS- directed antibody | protein | 224 | 9% helix, 50% strand | — |
| L, B | Light chain of Fab fragment of HIV vaccine-elicited CD4BS- directed antibody | protein | 212 | 6% helix, 51% strand | — |
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.58 | 0.76 | 49 | empty |
| 2 | 160 | 0.50 | 0.78 | 26 | empty |
| 3 | 147 | 0.50 | 0.79 | 22 | empty |
| 4 | 229 | 0.49 | 0.75 | 39 | empty |
| 5 | 93 | 0.41 | 0.78 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1795 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 1742 Ų buried · 20 hydrogen bonds · protein-protein
- L–A · 627 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4Q2Z · Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE356, from a non-human… · 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 4Q2Z · PDBe 4Q2Z
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