MolNFT v1 · #122086 · protein
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 2.16 a
5IES · VRC01CHUGL2 Fab heavy chain: “Crystal structure of VRC01C-HUGL2 Fab from an HIV-1 naive donor in complex with with a germline-targeting…”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability 0.56). MolNFT v1 #122086 on…
- PDB
- 5IES
- Type
- protein
- Length
- 592 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VRC01CHUGL2 Fab heavy chain; VRC01CHUGL2 Fab light chain; Germline-targeting HIV-1 GP120…
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | VRC01CHUGL2 Fab heavy chain | protein | 219 | 10% helix, 52% strand | — |
| L | VRC01CHUGL2 Fab light chain | protein | 206 | 7% helix, 52% strand | — |
| C | Germline-targeting HIV-1 GP120 engineered outer domain eod- GT8 | protein | 167 | 22% helix, 39% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C
- GOL · Glycerol · additive · 3 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.56 | 0.82 | 26 | empty |
| 2 | 285 | 0.53 | 0.75 | 43 | GOL |
| 3 | 121 | 0.50 | 0.80 | 34 | empty |
| 4 | 82 | 0.40 | 0.78 | 19 | empty |
| 5 | 79 | 0.37 | 0.77 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1801 Ų buried · 17 hydrogen bonds · protein-protein
- H–C · 812 Ų buried · 17 hydrogen bonds · protein-protein
- L–C · 394 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5IES · Crystal structure of VRC01c-HuGL2 Fab from an HIV-1 naive donor in complex with with 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 5IES · PDBe 5IES
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