MolNFT v1 · #19175 · protein
The crystal structure of the SIV GP41 ectodomain at 1.47 a
1QBZ · Protein (SIV GP41 ectodomain): “The crystal structure of the SIV GP41 ectodomain at 1.47 a”. X-ray diffraction, 2 ligands (HG, CL), 3 pockets (best druggability 0.52). MolNFT v1 #19175 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1QBZ
- Type
- protein
- Length
- 336 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (SIV GP41 ectodomain)
- Ligands
- HG, CL
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 89% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (SIV GP41 ectodomain) | protein | 102 | 95% helix, 0% strand | — |
| B | Protein (SIV GP41 ectodomain) | protein | 114 | 88% helix, 0% strand | — |
| C | Protein (SIV GP41 ectodomain) | protein | 120 | 86% helix, 0% strand | — |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains B, C
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.52 | 0.81 | 19 | empty |
| 2 | 95 | 0.40 | 0.77 | 23 | CL |
| 3 | 81 | 0.39 | 0.78 | 19 | CL |
Interfaces
3 interfaces between chains.
- B–C · 1828 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1764 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1603 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1QBZ · The crystal structure of the SIV GP41 ectodomain at 1.47 a · 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 1QBZ · PDBe 1QBZ
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