MolNFT v1 · #159834 · protein + DNA
Structure of HIV-1 reverse transcriptase (rt) in complex with dsdna and D-ddctp
6P2G · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “Structure of HIV-1 reverse transcriptase (rt) in complex with dsdna and D-ddctp”. X-ray diffraction, 3 ligands (DCT, MG, SO4), 15 pockets (best druggability 0.84). MolNFT v1 #159834 on…
- PDB
- 6P2G
- Type
- protein + DNA
- Length
- 973 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; P51 rt; DNA primer 20-mer; DNA template 27-mer
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13
- UniProt
- P04585
- Ligands
- DCT, MG, SO4
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 4 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) | protein | 545 | 32% helix, 23% strand | P04585 |
| B | P51 rt | protein | 388 | 37% helix, 20% strand | P04585 |
| P | DNA primer 20-mer | dna | 18 | — | — |
| T | DNA template 27-mer | dna | 22 | — | — |
Ligands and binding sites
- DCT · 2',3'-dideoxycytidine 5'-triphosphate · ligand · chains A, P, T
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains P, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.84 | 0.86 | 77 | empty |
| 2 | 1082 | 0.83 | 0.84 | 91 | empty |
| 3 | 513 | 0.71 | 0.80 | 39 | empty |
| 4 | 496 | 0.69 | 0.79 | 47 | empty |
| 5 | 251 | 0.59 | 0.79 | 39 | DCT, MG |
Interfaces
6 interfaces between chains.
- A–B · 2963 Ų buried · 33 hydrogen bonds · protein-protein
- A–T · 1204 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–P · 961 Ų buried · 11 hydrogen bonds · protein-nucleic
- P–T · 847 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- B–P · 90 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6P2G · Structure of HIV-1 Reverse Transcriptase (RT) in complex with dsDNA and D-ddCTP · the same entry in another collection · chain B against B, 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 6P2G · PDBe 6P2G · UniProt P04585
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