Research workbench
Fab fragment of HIV vaccine-elicited CD4BS-directed antibody, GE136, from non-human primate
Analyse Fab fragment of HIV vaccine-elicited CD4BS-directed antibody, GE136, from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KTD
- Type
- protein
- Length
- 433 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GE136 heavy chain Fab; GE136 light chain Fab
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | GE136 heavy chain Fab | protein | 217 | 6% helix, 57% strand | — |
| L | GE136 light chain Fab | protein | 216 | 9% helix, 53% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.63 | 0.75 | 61 | GOL |
| 2 | 60 | 0.38 | 0.80 | 16 | empty |
| 3 | 80 | 0.36 | 0.76 | 21 | SO4 |
| 4 | 56 | 0.34 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- H–L · 1795 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4KTD · Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE136, from 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 4KTD · PDBe 4KTD
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