Research workbench
HIV-1 reverse transcriptase-DNA complex with datp bound in the nucleotide binding site
Analyse HIV-1 reverse transcriptase-DNA complex with datp bound in the nucleotide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KK2
- Type
- protein + DNA
- Length
- 1,011 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
- DTP, MG, SO4
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse transcriptase P66 subunit (EC 2.7.7.49) | protein | 555 | 32% helix, 23% strand | P04585 |
| B | Reverse transcriptase P51 subunit (EC 2.7.7.49) | protein | 414 | 36% helix, 20% strand | P04585 |
| P | 5'-D(*AP*CP*A*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP* CP*CP*(DOC))-3' | dna | 18 | — | — |
| T | 5'-D(*A*TP*GP*GP*TP*GP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP* GP*GP*GP*AP*CP*TP*GP*TP*G)-3' | dna | 24 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, P, T
- MG · Magnesium ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, P, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.85 | 0.86 | 89 | MG |
| 2 | 1184 | 0.83 | 0.84 | 98 | empty |
| 3 | 464 | 0.75 | 0.84 | 48 | empty |
| 4 | 501 | 0.71 | 0.80 | 47 | empty |
| 5 | 468 | 0.69 | 0.80 | 51 | MG, DTP, SO4 |
Interfaces
6 interfaces between chains.
- A–B · 2998 Ų buried · 37 hydrogen bonds · protein-protein
- A–T · 1321 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–P · 957 Ų buried · 13 hydrogen bonds · protein-nucleic
- P–T · 835 Ų buried · 79 hydrogen bonds · nucleic-nucleic
- B–P · 101 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3KK2 · HIV-1 reverse transcriptase-DNA complex with dATP bound in the nucleotide binding site · 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 3KK2 · PDBe 3KK2 · UniProt P04585
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