Research workbench
Structure of the GP41 N-peptide in complex with the HIV entry inhibitor PIE1
Analyse Structure of the GP41 N-peptide in complex with the HIV entry inhibitor PIE1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R3C
- Type
- protein
- Length
- 116 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GP41 N-peptide; HIV entry inhibitor PIE1
- Ligands
- ACE, YT3, NH2, CL
- Pockets
- 1 · best druggability 0.25
Structure
x-ray diffraction · 4 distinct chains · 88% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GP41 N-peptide | protein | 45 | 96% helix, 0% strand | — |
| B | GP41 N-peptide | protein | 42 | 95% helix, 0% strand | — |
| C | HIV entry inhibitor PIE1 | protein | 14 | 57% helix, 0% strand | — |
| D | HIV entry inhibitor PIE1 | protein | 15 | 73% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A
- YT3 · Yttrium (III) ion · metal · 5 copies · chains A, C, B, D
- NH2 · Amino group · ion · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.25 | 0.73 | 13 | NH2 |
Interfaces
5 interfaces between chains.
- A–C · 301 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 299 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 295 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 277 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 26 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 d-amino, 2 disulfide, 1 covalent (D-amino acid, disulfide, covalent ligand).
Compared structures
- 2R3C · Structure of the gp41 N-peptide in complex with the HIV entry inhibitor PIE1 · 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 2R3C · PDBe 2R3C
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