MolNFT v1 · #62614 · protein
Crystal structure of the inhibitor amprenavir (apv) in complex with a multi-drug resistant HIV-1 protease variant (L10I/G48V/I54V/V64I/V82A)REFER: flap+ in citation
3EKP: “Crystal structure of the inhibitor amprenavir (apv) in complex with a multi-drug resistant HIV-1 protease…”. X-ray diffraction, 2 ligands (478, PO4), 2 pockets (best druggability 0.72). MolNFT v1 #62614 on GenesisL1: 3D structure…
- PDB
- 3EKP
- 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
- 478, PO4
- Pockets
- 2 · 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, C, D | Protease (EC 3.4.23.16) | protein | 99 | 6% helix, 55% strand | P03369 |
Ligands and binding sites
- 478 · {3-[(4-amino-benzenesulfonyl)-isobutyl-amino]-1-benzyl-2-hydroxy-propyl}-carbamic acid tetrahydro-furan-3-yl ester · ligand · 2 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- ACT · Acetate ion · additive · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.72 | 0.83 | 39 | 478 |
| 2 | 395 | 0.71 | 0.83 | 35 | 478 |
Interfaces
2 interfaces between chains.
- C–D · 1914 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1805 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 3EKP · Crystal Structure of the inhibitor Amprenavir (APV) in complex with a multi-drug… · 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 3EKP · PDBe 3EKP · UniProt P03369
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