Research workbench
Crystal structure of a late fusion intermediate of HIV-1 GP41
Analyse Crystal structure of a late fusion intermediate of HIV-1 GP41 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X7R
- Type
- protein
- Length
- 293 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transmembrane protein GP41
- UniProt
- P04578
- Ligands
- NA, CL
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 88% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transmembrane protein GP41 | protein | 39 | 92% helix, 0% strand | P04578 |
| B | Transmembrane protein GP41 | protein | 43 | 95% helix, 0% strand | P04578 |
| C | Transmembrane protein GP41 | protein | 58 | 88% helix, 0% strand | P04578 |
| D | Transmembrane protein GP41 | protein | 48 | 85% helix, 0% strand | P04578 |
| E | Transmembrane protein GP41 | protein | 54 | 87% helix, 0% strand | P04578 |
| N | Transmembrane protein GP41 | protein | 51 | 84% helix, 0% strand | P04578 |
Ligands and binding sites
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 | 585 | 0.70 | 0.79 | 45 | empty |
| 2 | 91 | 0.32 | 0.73 | 18 | empty |
| 3 | 50 | 0.26 | 0.73 | 9 | empty |
Interfaces
10 interfaces between chains.
- C–N · 1111 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 1066 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 936 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 378 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 358 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2X7R · Crystal structure of a late fusion intermediate of HIV-1 gp41 · 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
- Every structure of UniProt P04578
- Elsewhere: RCSB PDB 2X7R · PDBe 2X7R · UniProt P04578
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