MolNFT v1 · #63279 · protein
Trimeric helix bundle formed by an ALPHA/BETA-peptide derivative of the HIV GP41 chr domain
3F4Z · ALPHA/BETA-peptide analogue of the HIV GP41 chr domain: “Trimeric helix bundle formed by an ALPHA/BETA-peptide derivative of the HIV GP41 chr domain”. X-ray diffraction, 2 ligands (ACE, NH2), 2 pockets (best druggability 0.49).…
- PDB
- 3F4Z
- Type
- protein
- Length
- 110 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ALPHA/BETA-peptide analogue of the HIV GP41 chr domain
- Ligands
- ACE, NH2
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 93% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | ALPHA/BETA-peptide analogue of the HIV GP41 chr domain | protein | 38 | 92% helix, 0% strand | — |
| B | ALPHA/BETA-peptide analogue of the HIV GP41 chr domain | protein | 34 | 94% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C
- NH2 · Amino group · ion · chains C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.49 | 0.82 | 18 | MPD |
| 2 | 54 | 0.45 | 0.83 | 11 | empty |
Interfaces
3 interfaces between chains.
- B–C · 753 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 634 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 495 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified, 1 covalent (nonstandard, covalent ligand).
Compared structures
- 3F4Z · Trimeric helix bundle formed by an alpha/beta-peptide derivative of the HIV gp41 CHR… · the same entry in another collection · chain B against B, TM-score 0.96
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3F4Z · PDBe 3F4Z
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