MolNFT v1 · #145178 · protein
Crystal structure of HIV-1 Y188L mutant reverse transcriptase in complex with non-nucleoside inhibitor K-5A2
6CGF · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “Crystal structure of HIV-1 Y188L mutant reverse transcriptase in complex with non-nucleoside inhibitor K-5A2”. X-ray diffraction, 4 ligands (K5A, MG, NA), 13 pockets (best druggability 0.82).…
- PDB
- 6CGF
- Type
- protein
- Length
- 970 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; P51 rt
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
- UniProt
- P03366
- Ligands
- K5A, MG, NA, SO4
- Pockets
- 13 · 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, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 556 | 32% helix, 24% strand | P03366 |
| B | P51 rt (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 · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 23 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.82 | 0.83 | 101 | K5A, EDO |
| 2 | 686 | 0.77 | 0.82 | 64 | EDO, SO4 |
| 3 | 702 | 0.70 | 0.77 | 51 | EDO |
| 4 | 254 | 0.66 | 0.83 | 36 | SO4, EDO |
| 5 | 260 | 0.56 | 0.77 | 42 | EDO |
Interfaces
1 interface between chains.
- A–B · 2726 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6CGF · Crystal structure of HIV-1 Y188L 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 6CGF · PDBe 6CGF · UniProt P03366
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