Research workbench
HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:DGTP ternary complex
Analyse HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:DGTP ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KDN
- 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
- DGT, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 23% 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, 22% strand | P12497 |
| E | DNA/RNA (38-mer) | dna | 35 | — | — |
| F | DNA/RNA (38-mer) | dna | 38 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 2 copies · chains A, E, C, F
- MG · Magnesium ion · metal · 2 copies · chains A, C
- GOL · Glycerol · additive · 5 copies · chains A, E, B, 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 | 872 | 0.85 | 0.87 | 105 | GOL |
| 2 | 910 | 0.84 | 0.86 | 106 | GOL |
| 3 | 1148 | 0.83 | 0.84 | 86 | empty |
| 4 | 427 | 0.81 | 0.89 | 58 | GOL |
| 5 | 464 | 0.76 | 0.85 | 49 | empty |
Interfaces
7 interfaces between chains.
- C–D · 2987 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2976 Ų buried · 31 hydrogen bonds · protein-protein
- C–F · 1994 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–E · 1880 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–C · 817 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6KDN · HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:dGTP ternary complex · 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 6KDN · PDBe 6KDN · UniProt D3XFN5 · UniProt P12497
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