Research workbench
Crystal structure of HIV-1 clade C strain C1086 GP120 core in complex with nbd-556
Analyse Crystal structure of HIV-1 clade C strain C1086 GP120 core 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
- 3TGS
- Type
- protein
- Length
- 690 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 clade C1086 GP120 core
- Ligands
- 03G, NAG
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | HIV-1 clade C1086 GP120 core | protein | 345 | 16% helix, 33% strand | — |
Ligands and binding sites
- 03G · N-(4-chlorophenyl)-N'-(2,2,6,6-tetramethylpiperidin-4-yl)ethanediamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.76 | 0.82 | 79 | NAG |
| 2 | 81 | 0.57 | 0.87 | 22 | 03G |
| 3 | 70 | 0.56 | 0.88 | 22 | 03G |
| 4 | 114 | 0.55 | 0.83 | 22 | NAG |
| 5 | 147 | 0.54 | 0.81 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 446 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 13 glycan (disulfide, N-glycosylation).
Compared structures
- 3TGS · Crystal structure of HIV-1 clade C strain C1086 gp120 core in complex with NBD-556 · 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 3TGS · PDBe 3TGS
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