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Structure of HIV-1 reverse transcriptase (rt) ternary complex with a double stranded DNA and an incoming D4TTP at pH 7.0
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
- 6AMO
- Type
- protein + DNA
- Length
- 2,008 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
- D4T, MG
- Pockets
- 20 · best druggability 0.85
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, 2.7.7.7) | protein | 555 | 31% helix, 24% strand | P03366 |
| B | HIV-1 reverse transcriptase P51 subunit (EC 2.7.7.49, 2.7.7.7) | protein | 412 | 35% helix, 20% strand | P03366 |
| T, E | DNA (27-mer) | dna | 22 | — | — |
| P, F | DNA (5'- D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*(DDG))- 3') | dna | 20 | — | — |
| D | HIV-1 reverse transcriptase P51 subunit (EC 2.7.7.49, 2.7.7.7) | protein | 402 | 36% helix, 19% strand | P03366 |
Ligands and binding sites
- D4T · 2',3'-dehydro-2',3'-deoxy-thymidine 5'-triphosphate · ligand · 2 copies · chains A, T, P, C, E, F
- MG · Magnesium ion · metal · 4 copies · chains A, C
- GOL · Glycerol · additive · 13 copies · chains A, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 809 | 0.85 | 0.88 | 96 | GOL |
| 2 | 647 | 0.84 | 0.89 | 66 | empty |
| 3 | 372 | 0.82 | 0.91 | 41 | GOL |
| 4 | 336 | 0.81 | 0.91 | 31 | empty |
| 5 | 423 | 0.79 | 0.87 | 49 | empty |
Interfaces
13 interfaces between chains.
- A–B · 2955 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2887 Ų buried · 32 hydrogen bonds · protein-protein
- C–E · 1280 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–T · 1277 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–P · 970 Ų buried · 20 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6AMO · 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 6AMO · PDBe 6AMO · UniProt P03366
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