Research workbench
Apo HIV protease (pr) dimer in closed form with fragment 1F1-N in the OUTSIDE/TOP of flap
Analyse Apo HIV protease (pr) dimer in closed form with fragment 1F1-N in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EJL
- Type
- protein
- Length
- 198 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease
- EC
- 3.4.23.16
- UniProt
- P12499
- Ligands
- IOP
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protease (EC 3.4.23.16) | protein | 99 | 7% helix, 57% strand | P12499 |
Ligands and binding sites
- IOP · Indolylpropionic acid · ligand · chains A
- GOL · Glycerol · additive · 4 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.69 | 0.83 | 35 | GOL |
Interfaces
1 interface between chains.
- A–B · 1835 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 4EJL · Apo HIV Protease (PR) dimer in closed form with fragment 1F1-N in the outside/top of flap · 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 P12499
- Elsewhere: RCSB PDB 4EJL · PDBe 4EJL · UniProt P12499
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