MolNFT v1 · #159816 · protein + DNA
Structure of HIV-1 reverse transcriptase (rt) in complex with dsdna and L-ddctp
6P1X · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “Structure of HIV-1 reverse transcriptase (rt) in complex with dsdna and L-ddctp”. X-ray diffraction, 3 ligands (NQ4, MG, SO4), 18 pockets (best druggability 0.85). MolNFT v1 #159816 on…
- PDB
- 6P1X
- Type
- protein + DNA
- Length
- 1,005 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
- NQ4, MG, SO4
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 35% 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 | 557 | 32% helix, 23% strand | P04585 |
| B | P51 rt | protein | 406 | 38% helix, 20% strand | P04585 |
| P | DNA primer 20-mer | dna | 18 | — | — |
| T | DNA template 27-mer | dna | 24 | — | — |
Ligands and binding sites
- NQ4 · [[(2~{R},5~{S})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate · ligand · chains A, P, T
- MG · Magnesium ion · metal · 2 copies · chains A, T
- SO4 · Sulfate ion · ion · 3 copies · chains P, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.85 | 0.88 | 69 | MG |
| 2 | 786 | 0.84 | 0.87 | 81 | empty |
| 3 | 471 | 0.70 | 0.80 | 40 | empty |
| 4 | 556 | 0.68 | 0.78 | 52 | empty |
| 5 | 421 | 0.68 | 0.80 | 38 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2927 Ų buried · 36 hydrogen bonds · protein-protein
- A–T · 1300 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–P · 1004 Ų buried · 13 hydrogen bonds · protein-nucleic
- P–T · 847 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- B–P · 76 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6P1X · Structure of HIV-1 Reverse Transcriptase (RT) in complex with dsDNA and L-ddCTP · 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 P04585
- Elsewhere: RCSB PDB 6P1X · PDBe 6P1X · UniProt P04585
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