Research workbench
Crystal structure of HIV-1 reverse transcriptase (rt) with DNA and the nonnucleoside inhibitor nevirapine
Analyse Crystal structure of HIV-1 reverse transcriptase (rt) with DNA and the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V81
- Type
- protein + DNA
- Length
- 2,014 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
- NVP
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 19% 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, 20% 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 | 20 | — | — |
| P, F | DNA (5'- D(*A*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
- NVP · 11-cyclopropyl-5,11-dihydro-4-methyl-6H-dipyrido[3,2-B:2',3'-e][1,4]diazepin-6-one · ligand · 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 | 1158 | 0.87 | 0.88 | 121 | empty |
| 2 | 685 | 0.85 | 0.90 | 73 | empty |
| 3 | 481 | 0.81 | 0.89 | 58 | empty |
| 4 | 753 | 0.79 | 0.82 | 74 | NVP |
| 5 | 950 | 0.78 | 0.80 | 90 | empty |
Interfaces
14 interfaces between chains.
- A–B · 2809 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2681 Ų buried · 33 hydrogen bonds · protein-protein
- C–F · 992 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–P · 941 Ų buried · 12 hydrogen bonds · protein-nucleic
- T–P · 939 Ų buried · 89 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 3V81 · Crystal structure of HIV-1 reverse transcriptase (RT) with DNA and the nonnucleoside… · 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 3V81 · PDBe 3V81 · UniProt P03366
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