MolNFT v1 · #69216 · protein + DNA
HIV-1 reverse transcriptase in complex with DNA
3KJV · Reverse transcriptase P66 subunit: “HIV-1 reverse transcriptase in complex with DNA”. X-ray diffraction, 2 ligands (MG, SO4), 17 pockets (best druggability 0.86). MolNFT v1 #69216 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3KJV
- Type
- protein + DNA
- Length
- 990 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
- MG, SO4
- Pockets
- 17 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse transcriptase P66 subunit (EC 2.7.7.49) | protein | 549 | 29% helix, 19% strand | P04585 |
| B | Reverse transcriptase P51 subunit (EC 2.7.7.49) | protein | 400 | 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*CP*(DOC))-3' | dna | 18 | — | — |
| T | 5'-D(*AP*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 | 23 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.86 | 0.89 | 93 | empty |
| 2 | 417 | 0.83 | 0.91 | 41 | empty |
| 3 | 511 | 0.71 | 0.80 | 49 | empty |
| 4 | 442 | 0.70 | 0.81 | 47 | empty |
| 5 | 542 | 0.65 | 0.76 | 53 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2948 Ų buried · 32 hydrogen bonds · protein-protein
- A–T · 1273 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–P · 925 Ų buried · 9 hydrogen bonds · protein-nucleic
- P–T · 827 Ų buried · 71 hydrogen bonds · nucleic-nucleic
- B–P · 91 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3KJV · HIV-1 reverse transcriptase in complex with 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 P04585
- Elsewhere: RCSB PDB 3KJV · PDBe 3KJV · UniProt P04585
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