Research workbench
Crystal structure of HIV-1 CA146 A92E real cell
Analyse Crystal structure of HIV-1 CA146 A92E real cell in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PWM
- Type
- protein
- Length
- 1,144 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gag-pol polyprotein
- UniProt
- P12497
- Ligands
- CL
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, G, H | Gag-pol polyprotein | protein | 145 | 57% helix, 4% strand | P12497 |
| B, F | Gag-pol polyprotein | protein | 137 | 61% helix, 4% strand | P12497 |
Ligands and binding sites
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.75 | 0.81 | 72 | CL |
| 2 | 567 | 0.75 | 0.82 | 60 | CL |
| 3 | 699 | 0.74 | 0.80 | 60 | CL |
| 4 | 688 | 0.73 | 0.79 | 60 | CL |
| 5 | 459 | 0.68 | 0.80 | 52 | empty |
Interfaces
12 interfaces between chains.
- E–F · 1056 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1017 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 978 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 968 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 601 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2PWM · Crystal Structure of HIV-1 CA146 A92E real cell · 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 P12497
- Elsewhere: RCSB PDB 2PWM · PDBe 2PWM · UniProt P12497
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