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Crystal structure of HIV-1 reverse transcriptase (rt) in complex with a double stranded RNA represents the rt transcription initiation complex prior to nucleotide incorporation
Analyse Crystal structure of HIV-1 reverse transcriptase (rt) in 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
- 6HAK
- Type
- protein + RNA
- Length
- 2,007 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gag-pol polyprotein; RNA (5'- R(P*AP*GP*UP*GP*GP*CP*GP*GP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP…
- EC
- 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2, 2.7.7.-, 3.1.-.-
- UniProt
- P03366
- Ligands
- GLC, FRU, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Gag-pol polyprotein (EC 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2, 2.7.7.-, 3.1.-.-) | protein | 553 | 30% helix, 22% strand | P03366 |
| B | Gag-pol polyprotein (EC 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2, 2.7.7.-, 3.1.-.-) | protein | 412 | 33% helix, 16% strand | P03366 |
| T, E | RNA (5'- R(P*AP*GP*UP*GP*GP*CP*GP*GP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C)-3') | rna | 20 | — | — |
| P, F | RNA (5'- R(P*UP*CP*CP*CP*UP*GP*UP*UP*CP*GP*GP*CP*CP*GP*CP*CP*A)-3') | rna | 17 | — | — |
| D | Gag-pol polyprotein (EC 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2, 2.7.7.-, 3.1.-.-) | protein | 415 | 33% helix, 16% strand | P03366 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · chains B
- FRU · beta-D-fructofuranose · sugar · chains B, P
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.87 | 0.88 | 94 | empty |
| 2 | 1166 | 0.87 | 0.88 | 116 | GLC, FRU |
| 3 | 1147 | 0.81 | 0.83 | 85 | empty |
| 4 | 1110 | 0.80 | 0.82 | 109 | empty |
| 5 | 160 | 0.79 | 0.95 | 31 | empty |
Interfaces
13 interfaces between chains.
- C–D · 2985 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2941 Ų buried · 18 hydrogen bonds · protein-protein
- A–T · 992 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–E · 978 Ų buried · 6 hydrogen bonds · protein-nucleic
- T–P · 892 Ų buried · 101 hydrogen bonds · nucleic-nucleic
Compared structures
- 6HAK · Crystal structure of HIV-1 reverse transcriptase (RT) in complex with a double stranded… · 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 6HAK · PDBe 6HAK · UniProt P03366
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