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Structure of HIV-1 reverse transcriptase (rt) ternary complex with a double stranded DNA and an incoming ddatp
Analyse Structure of HIV-1 reverse transcriptase (rt) ternary complex with a double… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TXM
- Type
- protein + DNA
- Length
- 2,023 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 reverse transcriptase P66 subunit; HIV-1 reverse transcriptase P51 subunit; DNA…
- EC
- 2.7.7.49, 2.7.7.7
- UniProt
- P03366
- Ligands
- DDS, GLC, FRU, MG, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HIV-1 reverse transcriptase P66 subunit (EC 2.7.7.49) | protein | 556 | 33% helix, 23% strand | P03366 |
| B | HIV-1 reverse transcriptase P51 subunit (EC 2.7.7.7) | protein | 411 | 36% helix, 20% strand | P03366 |
| T, E | DNA (5'- D(*TP*GP*GP*TP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP* TP*G)-3') | dna | 24 | — | — |
| P, F | DNA (5'-D(*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG) P*CP*GP*CP*CP*G)-3') | dna | 20 | — | — |
| D | HIV-1 reverse transcriptase P51 subunit (EC 2.7.7.7) | protein | 412 | 35% helix, 20% strand | P03366 |
Ligands and binding sites
- DDS · 2',3'-dideoxyadenosine triphosphate · ligand · 2 copies · chains A, T, P, C, E, F
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains B, D
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains B, D, F
- MG · Magnesium ion · metal · 4 copies · chains A, C
- SO4 · Sulfate ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, T, P, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.87 | 0.88 | 93 | EDO |
| 2 | 605 | 0.83 | 0.89 | 67 | empty |
| 3 | 1122 | 0.83 | 0.84 | 97 | GLC, FRU, SO4 |
| 4 | 363 | 0.81 | 0.90 | 34 | empty |
| 5 | 1138 | 0.76 | 0.78 | 90 | empty |
Interfaces
14 interfaces between chains.
- A–B · 2957 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2939 Ų buried · 34 hydrogen bonds · protein-protein
- A–T · 1389 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–E · 1271 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–P · 1020 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5TXM · Structure of HIV-1 reverse transcriptase (rt) ternary complex with a double stranded DNA… · 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 P03366
- Elsewhere: RCSB PDB 5TXM · PDBe 5TXM · UniProt P03366
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