Research workbench
Crystal structure of unbound VRC01C-HUGL2 Fab from an HIV-1 naive donor at 1.82 a
Analyse Crystal structure of unbound VRC01C-HUGL2 Fab from an HIV-1 naive donor at 1.82… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IFA
- Type
- protein
- Length
- 426 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VRC01C-HUGL2 Fab heavy chain; VRC01C-HUGL2 Fab light chain
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | VRC01C-HUGL2 Fab heavy chain | protein | 219 | 10% helix, 52% strand | — |
| L | VRC01C-HUGL2 Fab light chain | protein | 207 | 7% helix, 51% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains H, L
- GOL · Glycerol · additive · 7 copies · chains H, L
- 1PE · Pentaethylene glycol · additive · 4 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 578 | 0.63 | 0.75 | 60 | GOL |
| 2 | 81 | 0.34 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- H–L · 1829 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, additive adduct).
Compared structures
- 5IFA · Crystal structure of unbound VRC01c-HuGL2 Fab from an HIV-1 naive donor at 1.82 A · 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 5IFA · PDBe 5IFA
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