MolNFT v1 · #168727 · protein + DNA
Structure of HIV-1 reverse transcriptase (rt) in complex with dsdna and D4T
6WPF · DNA primer 21-mer: “Structure of HIV-1 reverse transcriptase (rt) in complex with dsdna and D4T”. X-ray diffraction, 4 ligands (D4M, D4T, MG), 16 pockets (best druggability 0.86). MolNFT v1 #168727 on GenesisL1: 3D structure…
- PDB
- 6WPF
- Type
- protein + DNA
- Length
- 990 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA primer 21-mer; DNA template 27-mer; Reverse TRANSCRIPTASE/RIBONUCLEASE H; P51 rt
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.-.-
- UniProt
- P04585
- Ligands
- D4M, D4T, MG, SO4
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | DNA primer 21-mer | dna | 18 | — | — |
| T | DNA template 27-mer | dna | 23 | — | — |
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 555 | 32% helix, 24% strand | P04585 |
| B | P51 rt (EC 2.7.7.-, 3.1.-.-) | protein | 394 | 37% helix, 21% strand | P04585 |
Ligands and binding sites
- D4M · [(5R)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2,5-dihydrofuran-2-yl]methyl dihydrogen phosphate · ligand · chains P, A
- D4T · 2',3'-dehydro-2',3'-deoxy-thymidine 5'-triphosphate · ligand · chains P, T, A
- MG · Magnesium ion · metal · 3 copies · chains P, A
- SO4 · Sulfate ion · ion · 4 copies · chains P, T, A, B
- GOL · Glycerol · additive · 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 693 | 0.86 | 0.90 | 82 | empty |
| 2 | 482 | 0.82 | 0.89 | 55 | GOL |
| 3 | 510 | 0.71 | 0.80 | 40 | empty |
| 4 | 494 | 0.69 | 0.80 | 48 | empty |
| 5 | 296 | 0.68 | 0.83 | 39 | D4M, MG, D4T |
Interfaces
6 interfaces between chains.
- A–B · 2974 Ų buried · 33 hydrogen bonds · protein-protein
- T–A · 1276 Ų buried · 10 hydrogen bonds · protein-nucleic
- P–A · 1029 Ų buried · 9 hydrogen bonds · protein-nucleic
- P–T · 837 Ų buried · 62 hydrogen bonds · nucleic-nucleic
- P–B · 96 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 6WPF · Structure of HIV-1 Reverse Transcriptase (RT) in complex with dsDNA and d4T · the same entry in another collection · chain P against P, 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 P04585
- Elsewhere: RCSB PDB 6WPF · PDBe 6WPF · UniProt P04585
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