MolNFT v1 · #15839 · protein
1.03 a structure of HIV-1 protease: inhibitor binding inside and outside the active site
1NH0 · Protease retropepsin: “1.03 a structure of HIV-1 protease: inhibitor binding inside and outside the active site”. X-ray diffraction, 3 ligands (KI2, NH2, SO4), 1 pocket (best druggability 0.60). MolNFT v1 #15839 on GenesisL1: 3D…
- PDB
- 1NH0
- Type
- protein
- Length
- 204 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease retropepsin; Peptidomimetic inhibitor KI2-phe-glu-glu-NH2
- EC
- 3.4.23.16
- UniProt
- P03367
- Ligands
- KI2, NH2, SO4
- Pockets
- 1 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protease retropepsin (EC 3.4.23.16) | protein | 99 | 7% helix, 55% strand | P03367 |
| I, J | Peptidomimetic inhibitor KI2-phe-glu-glu-NH2 | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- KI2 · 3-benzyloxycarbonylamino-2-hydroxy-4-phenyl-butyric acid · ligand · 2 copies · chains A, B, I, J
- NH2 · Amino group · ion · 2 copies · chains A, I, J
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · 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 | 200 | 0.60 | 0.81 | 24 | KI2 |
Interfaces
4 interfaces between chains.
- A–B · 1851 Ų buried · 39 hydrogen bonds · protein-protein
- A–I · 289 Ų buried · 9 hydrogen bonds · protein-protein
- B–I · 223 Ų buried · 2 hydrogen bonds · protein-protein
- A–J · 141 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (additive adduct, covalent ligand).
Compared structures
- 1NH0 · 1.03 A structure of HIV-1 protease: inhibitor binding inside and outside the active site · 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 P03367
- Elsewhere: RCSB PDB 1NH0 · PDBe 1NH0 · UniProt P03367
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