Research workbench
Crystal structure of VRC01C-HUGL2 Fab from an HIV-1 naive donor in complex with with a germline-targeting GP120 engineered outer domain eod-GT8 at 2.44 a
Analyse Crystal structure of VRC01C-HUGL2 Fab from an HIV-1 naive donor in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IF0
- Type
- protein
- Length
- 1,188 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VRC01CHUGL2 Fab heavy chain; VRC01C-HUGL2 Fab light chain; Germline-targeting HIV-1 GP120…
- Ligands
- NAG, PO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | VRC01CHUGL2 Fab heavy chain | protein | 219 | 8% helix, 52% strand | — |
| B, L | VRC01C-HUGL2 Fab light chain | protein | 206 | 7% helix, 52% strand | — |
| G, I | Germline-targeting HIV-1 GP120 engineered outer domain eod- GT8 | protein | 169 | 21% helix, 39% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains G, I
- PO4 · Phosphate ion · ion · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.78 | 0.85 | 82 | empty |
| 2 | 138 | 0.63 | 0.86 | 29 | empty |
| 3 | 298 | 0.62 | 0.80 | 35 | empty |
| 4 | 143 | 0.62 | 0.85 | 28 | empty |
| 5 | 183 | 0.59 | 0.82 | 26 | empty |
Interfaces
10 interfaces between chains.
- H–L · 1779 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1735 Ų buried · 12 hydrogen bonds · protein-protein
- B–L · 1115 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 836 Ų buried · 19 hydrogen bonds · protein-protein
- A–I · 829 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5IF0 · Crystal structure of VRC01c-HuGL2 Fab from an HIV-1 naive donor in complex with with a… · the same entry in another collection · chain A against A, 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 5IF0 · PDBe 5IF0
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