MolNFT v1 · #154514 · protein + DNA
HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:ENTECAVIR 5'- triphosphate ternary complex
6KDM · HIV-1 reverse transcriptase P66 subunit: “HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:ENTECAVIR 5'- triphosphate ternary complex”. X-ray diffraction, 2 ligands (ET9, MG), 20 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 6KDM
- Type
- protein + DNA
- Length
- 1,991 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 reverse transcriptase P66 subunit; HIV-1 rt P51 subunit; DNA/RNA (38-mer)
- UniProt
- D3XFN5, P12497
- Ligands
- ET9, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HIV-1 reverse transcriptase P66 subunit | protein | 553 | 33% helix, 24% strand | D3XFN5 |
| B, D | HIV-1 rt P51 subunit | protein | 406 | 34% helix, 20% strand | P12497 |
| E | DNA/RNA (38-mer) | dna | 35 | — | — |
| F | DNA/RNA (38-mer) | dna | 38 | — | — |
Ligands and binding sites
- ET9 · [[(1R,3S,5S)-3-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphory l] phosphono hydrogen phosphate · ligand · 2 copies · chains A, E, C, F
- MG · Magnesium ion · metal · 2 copies · chains A, C
- GOL · Glycerol · additive · 6 copies · chains A, B, E, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.84 | 0.85 | 96 | GOL |
| 2 | 817 | 0.84 | 0.86 | 92 | GOL |
| 3 | 672 | 0.83 | 0.88 | 74 | GOL |
| 4 | 667 | 0.83 | 0.87 | 78 | GOL |
| 5 | 527 | 0.77 | 0.84 | 54 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2985 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2960 Ų buried · 35 hydrogen bonds · protein-protein
- C–F · 1976 Ų buried · 32 hydrogen bonds · protein-nucleic
- A–E · 1910 Ų buried · 29 hydrogen bonds · protein-nucleic
- A–C · 789 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6KDM · HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:entecavir 5'-triphosphate ternary… · 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 D3XFN5
- Every structure of UniProt P12497
- Elsewhere: RCSB PDB 6KDM · PDBe 6KDM · UniProt D3XFN5 · UniProt P12497
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