Research workbench
Crystal structure of the outer domain of HIV-1 GP120 in complex with vrc-PG04 space group P3221
Analyse Crystal structure of the outer domain of HIV-1 GP120 in complex with vrc-PG04… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I3R
- Type
- protein
- Length
- 626 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer domain of HIV-1 GP120 (KER2018 OD4.2.2); Heavy chain of vrc-PG04 Fab; Light chain…
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Outer domain of HIV-1 GP120 (KER2018 OD4.2.2) | protein | 190 | 11% helix, 37% strand | — |
| H | Heavy chain of vrc-PG04 Fab | protein | 228 | 10% helix, 50% strand | — |
| L | Light chain of vrc-PG04 Fab | protein | 208 | 7% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.59 | 0.81 | 31 | empty |
| 2 | 329 | 0.54 | 0.74 | 47 | empty |
| 3 | 184 | 0.46 | 0.76 | 29 | empty |
| 4 | 107 | 0.40 | 0.76 | 18 | empty |
| 5 | 119 | 0.40 | 0.75 | 24 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1901 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 950 Ų buried · 18 hydrogen bonds · protein-protein
- G–L · 188 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4I3R · Crystal structure of the outer domain of HIV-1 gp120 in complex with VRC-PG04 space group… · the same entry in another collection · chain G against G, 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 4I3R · PDBe 4I3R
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