MolNFT v1 · #12514 · protein
Substrate shape determines specificity of recognition recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes
1KJ4 · Pol polyprotein: “Substrate shape determines specificity of recognition recognition for HIV-1 protease: analysis of crystal…”. X-ray diffraction, 2 pockets (best druggability 0.55). MolNFT v1 #12514 on GenesisL1: 3D structure…
- PDB
- 1KJ4
- Type
- protein
- Length
- 413 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pol polyprotein; Gag polyprotein
- EC
- 3.4.23.16
- UniProt
- P03369, P20875
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pol polyprotein (EC 3.4.23.16) | protein | 99 | 4% helix, 54% strand | P03369 |
| P | Gag polyprotein | protein | 9 | 0% helix, 56% strand | P20875 |
| S | Gag polyprotein | protein | 8 | 0% helix, 38% strand | P20875 |
Ligands and binding sites
- ACT · Acetate ion · additive · 12 copies · chains A, B, D, C, S
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 | 338 | 0.55 | 0.75 | 33 | ACT |
| 2 | 255 | 0.52 | 0.76 | 31 | ACT |
Interfaces
14 interfaces between chains.
- C–D · 1862 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 1809 Ų buried · 36 hydrogen bonds · protein-protein
- C–S · 533 Ų buried · 11 hydrogen bonds · protein-protein
- A–P · 532 Ų buried · 11 hydrogen bonds · protein-protein
- B–P · 525 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1KJ4 · Substrate shape determines specificity of recognition recognition for HIV-1 protease… · the same entry in another collection · chain P against P, 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
- Every structure of UniProt P20875
- Elsewhere: RCSB PDB 1KJ4 · PDBe 1KJ4 · UniProt P03369 · UniProt P20875
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