MolNFT v1 · #62663 · protein
Crystal structure of atazanavir (atv) in complex with I50L/A71V drug- resistant HIV-1 protease
3EM4: “Crystal structure of atazanavir (atv) in complex with I50L/A71V drug- resistant HIV-1 protease”. X-ray diffraction, 2 ligands (DR7, PO4), 4 pockets (best druggability 0.72). MolNFT v1 #62663 on GenesisL1: 3D structure, binding sites…
- PDB
- 3EM4
- Type
- protein
- Length
- 396 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease
- EC
- 3.4.23.16
- UniProt
- P03369
- Ligands
- DR7, PO4
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, U, V | Protease (EC 3.4.23.16) | protein | 99 | 6% helix, 55% strand | P03369 |
Ligands and binding sites
- DR7 · (3S,8S,9S,12S)-3,12-bis(1,1-dimethylethyl)-8-hydroxy-4,11-dioxo-9-(phenylmethyl)-6-[[4-(2-pyridinyl)phenyl]methyl]-2,5, 6,10,13-pentaazatetradecanedioic acid dimethyl ester · ligand · 2 copies · chains A, B, U, V
- PO4 · Phosphate ion · ion · 7 copies · chains A, B, U, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 456 | 0.72 | 0.82 | 38 | DR7 |
| 2 | 406 | 0.71 | 0.82 | 39 | DR7 |
| 3 | 208 | 0.49 | 0.75 | 26 | empty |
| 4 | 82 | 0.46 | 0.82 | 24 | empty |
Interfaces
6 interfaces between chains.
- U–V · 1820 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 1774 Ų buried · 40 hydrogen bonds · protein-protein
- B–V · 217 Ų buried · 0 hydrogen bonds · protein-protein
- A–U · 210 Ų buried · 0 hydrogen bonds · protein-protein
- B–U · 39 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3EM4 · Crystal structure of atazanavir (ATV) in complex with I50L/A71V drug-resistant HIV-1… · 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 P03369
- Elsewhere: RCSB PDB 3EM4 · PDBe 3EM4 · UniProt P03369
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