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HIV-1 reverse transcriptase complex with DNA and L-glutamate tenofovir with bound manganese
Analyse HIV-1 reverse transcriptase complex with DNA and L-glutamate tenofovir with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AIF
- Type
- protein + DNA
- Length
- 2,021 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gag-pol polyprotein; DNA (5'- D(P*GP*GP*TP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP…
- 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
- RE5, MN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 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 | 555 | 30% helix, 24% 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 | 411 | 35% helix, 20% strand | P03366 |
| 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 | 556 | 31% helix, 23% strand | P03366 |
| 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 | 412 | 35% helix, 19% strand | P03366 |
| T | DNA (5'- D(P*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 | 23 | — | — |
| 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*(DDG))-3') | dna | 20 | — | — |
| E | DNA (5'- D(P*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 | — | — |
Ligands and binding sites
- RE5 · L-Glutamate Tenofovir · ligand · 2 copies · chains A, T, P, C, E, F
- MN · Manganese (II) ion · metal · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1141 | 0.85 | 0.86 | 98 | empty |
| 2 | 486 | 0.84 | 0.90 | 55 | empty |
| 3 | 1124 | 0.84 | 0.85 | 85 | empty |
| 4 | 601 | 0.82 | 0.88 | 67 | empty |
| 5 | 625 | 0.81 | 0.86 | 57 | empty |
Interfaces
13 interfaces between chains.
- A–B · 2968 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2892 Ų buried · 30 hydrogen bonds · protein-protein
- C–E · 1369 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–T · 1317 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–P · 1014 Ų buried · 14 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 7AIF · HIV-1 reverse transcriptase complex with DNA and L-glutamate tenofovir with bound… · the same entry in another collection · chain F against F, 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 7AIF · PDBe 7AIF · UniProt P03366
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