MolNFT v1 · #81839 · protein + DNA
Crystal structure of HIV-1 reverse transcriptase (rt) with DNA and azttp
3V4I · HIV-1 reverse transcriptase P66 subunit: “Crystal structure of HIV-1 reverse transcriptase (rt) with DNA and azttp”. X-ray diffraction, 2 ligands (AZT, MG), 20 pockets (best druggability 0.87). MolNFT v1 #81839 on GenesisL1: 3D…
- PDB
- 3V4I
- Type
- protein + DNA
- Length
- 2,022 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 reverse transcriptase P66 subunit; HIV-1 reverse transcriptase P51 subunit; DNA…
- EC
- 2.7.7.49, 2.7.7.7
- UniProt
- P03366
- Ligands
- AZT, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HIV-1 reverse transcriptase P66 subunit (EC 2.7.7.49, 2.7.7.7) | protein | 555 | 32% helix, 23% strand | P03366 |
| B, D | HIV-1 reverse transcriptase P51 subunit (EC 2.7.7.49, 2.7.7.7) | protein | 412 | 35% helix, 19% strand | P03366 |
| T, E | DNA (5'- D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP* CP*TP*GP*TP*G)-3') | dna | 24 | — | — |
| P, F | DNA (5'- D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG) P*CP*GP*CP*CP*(ATM))-3') | dna | 20 | — | — |
Ligands and binding sites
- AZT · 3'-azido-3'-deoxythymidine-5'-triphosphate · ligand · 2 copies · chains A, T, P, C, E, F
- MG · Magnesium ion · metal · 2 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.87 | 0.88 | 99 | empty |
| 2 | 600 | 0.83 | 0.88 | 66 | empty |
| 3 | 400 | 0.82 | 0.91 | 46 | empty |
| 4 | 496 | 0.81 | 0.88 | 58 | empty |
| 5 | 318 | 0.81 | 0.92 | 31 | empty |
Interfaces
13 interfaces between chains.
- A–B · 2946 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2875 Ų buried · 37 hydrogen bonds · protein-protein
- A–T · 1369 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–E · 1333 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–F · 994 Ų buried · 16 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 3V4I · Crystal structure of HIV-1 reverse transcriptase (RT) with DNA and AZTTP · 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 3V4I · PDBe 3V4I · UniProt P03366
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