MolNFT v1 · #180352 · protein
Crystal structure of HIV-1 rt in complex with 16C (K07-15)
7KWU · Reverse transcriptase P66: “Crystal structure of HIV-1 rt in complex with 16C (K07-15)”. X-ray diffraction, 3 ligands (K7F, MG, SO4), 16 pockets (best druggability 0.82). MolNFT v1 #180352 on GenesisL1: 3D structure, binding sites…
- PDB
- 7KWU
- Type
- protein
- Length
- 970 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse transcriptase P66; Reverse transcriptase P51
- EC
- 2.7.7.49
- UniProt
- P03366
- Ligands
- K7F, MG, SO4
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse transcriptase P66 (EC 2.7.7.49) | protein | 556 | 32% helix, 24% strand | P03366 |
| B | Reverse transcriptase P51 | protein | 414 | 36% helix, 19% strand | P03366 |
Ligands and binding sites
- K7F · 4-[(4-{[4-(4-cyano-2,6-dimethylphenoxy)-5-(pyridin-4-yl)pyrimidin-2-yl]amino}piperidin-1-yl) methyl]benzamide · ligand · chains A, B
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1047 | 0.82 | 0.83 | 99 | EDO, K7F |
| 2 | 739 | 0.78 | 0.82 | 73 | SO4 |
| 3 | 782 | 0.72 | 0.78 | 58 | empty |
| 4 | 344 | 0.70 | 0.83 | 37 | SO4, EDO |
| 5 | 267 | 0.56 | 0.77 | 43 | EDO |
Interfaces
1 interface between chains.
- A–B · 2718 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 7KWU · Crystal Structure of HIV-1 RT in Complex with 16c (K07-15) · 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 P03366
- Elsewhere: RCSB PDB 7KWU · PDBe 7KWU · UniProt P03366
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