MolNFT v1 · #144666 · protein
Crystal structure of HIV-1 E138K mutant reverse transcriptase in complex with non-nucleoside inhibitor K-5A2
6C0L · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “Crystal structure of HIV-1 E138K mutant reverse transcriptase in complex with non-nucleoside inhibitor K-5A2”. X-ray diffraction, 4 ligands (K5A, MG, NA), 17 pockets (best druggability 0.82).…
- PDB
- 6C0L
- Type
- protein
- Length
- 970 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; Reverse transcriptase P51 subunit
- EC
- 2.7.7.49
- UniProt
- P03366
- Ligands
- K5A, MG, NA, SO4
- Pockets
- 17 · 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/RIBONUCLEASE H (EC 2.7.7.49) | protein | 556 | 32% helix, 24% strand | P03366 |
| B | Reverse transcriptase P51 subunit (EC 2.7.7.49) | protein | 414 | 36% helix, 19% strand | P03366 |
Ligands and binding sites
- K5A · 4-[(4-{[4-(4-cyano-2,6-dimethylphenoxy)thieno[3,2-d]pyrimidin-2-yl]amino}piperidin-1-yl)methyl]benzene-1-sulfonamide · ligand · chains A, B
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 26 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.82 | 0.83 | 89 | K5A, SO4, EDO |
| 2 | 695 | 0.77 | 0.82 | 65 | EDO, SO4 |
| 3 | 166 | 0.74 | 0.92 | 26 | EDO |
| 4 | 668 | 0.69 | 0.77 | 51 | EDO |
| 5 | 270 | 0.56 | 0.77 | 45 | EDO |
Interfaces
1 interface between chains.
- A–B · 2697 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6C0L · Crystal structure of HIV-1 E138K mutant reverse transcriptase in complex with… · 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 6C0L · PDBe 6C0L · UniProt P03366
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.