Research workbench
HIV-1 reverse transcriptase-DNA complex with gs-9148 terminated primer
Analyse HIV-1 reverse transcriptase-DNA complex with gs-9148 terminated primer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KK3
- Type
- protein + DNA
- Length
- 1,002 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse transcriptase P66 subunit; Reverse transcriptase P51 subunit…
- EC
- 2.7.7.49
- UniProt
- P04585
- Ligands
- URT, MG, SO4
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse transcriptase P66 subunit (EC 2.7.7.49) | protein | 555 | 30% helix, 22% strand | P04585 |
| B | Reverse transcriptase P51 subunit (EC 2.7.7.49) | protein | 407 | 31% helix, 20% strand | P04585 |
| P | 5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP *CP*C*(URT))-3' | dna | 17 | — | — |
| T | 5'-D(*AP*TP*GP*GP*TP*TP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP *GP*GP*GP*AP*CP*TP*GP*TP*G)-3' | dna | 23 | — | — |
Ligands and binding sites
- URT · ({[(2R,5R)-5-(6-amino-9H-purin-9-yl)-4-fluoro-2,5-dihydrofuran-2-yl]oxy}methyl)phosphonic acid · ligand · chains A, P, T
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains P, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.86 | 0.87 | 83 | empty |
| 2 | 639 | 0.84 | 0.89 | 73 | MG |
| 3 | 368 | 0.72 | 0.84 | 38 | empty |
| 4 | 499 | 0.69 | 0.79 | 41 | empty |
| 5 | 379 | 0.68 | 0.81 | 41 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3016 Ų buried · 34 hydrogen bonds · protein-protein
- A–T · 1393 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–P · 874 Ų buried · 12 hydrogen bonds · protein-nucleic
- P–T · 785 Ų buried · 81 hydrogen bonds · nucleic-nucleic
- B–T · 121 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3KK3 · HIV-1 reverse transcriptase-DNA complex with GS-9148 terminated primer · 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 3KK3 · PDBe 3KK3 · UniProt P04585
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