Research workbench
Crystal structure of HIV-1 reverse transcriptase in complex with bulge-RNA/DNA and nevirapine
Analyse Crystal structure of HIV-1 reverse transcriptase in complex with bulge-RNA/DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PWD
- Type
- protein + DNA + RNA
- Length
- 2,013 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…
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
- UniProt
- P03366
- Ligands
- NVP, CA, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 20% 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, 3.1.26.13, 3.1.13.2) | protein | 555 | 31% helix, 21% strand | P03366 |
| B, D | HIV-1 reverse transcriptase, P51 subunit (EC 2.7.7.49, 2.7.7.7) | protein | 412 | 36% helix, 20% strand | P03366 |
| T | 5'-R(*AP*UP*GP*GP*UP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*AP*CP *AP*GP*GP*GP*AP*CP*UP*GP*U)-3' | rna | 21 | — | — |
| E | 5'-R(*AP*UP*GP*GP*UP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*AP*CP *AP*GP*GP*GP*AP*CP*UP*GP*U)-3' | rna | 20 | — | — |
| P, F | 5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP* CP*CP*G)-3' | dna | 19 | — | — |
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
- CA · Calcium ion · metal · 2 copies · chains A, C, E
- SO4 · Sulfate ion · ion · chains B
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 | 1051 | 0.86 | 0.87 | 89 | empty |
| 2 | 630 | 0.84 | 0.89 | 62 | empty |
| 3 | 705 | 0.83 | 0.87 | 82 | empty |
| 4 | 739 | 0.79 | 0.83 | 72 | NVP |
| 5 | 1062 | 0.78 | 0.80 | 99 | empty |
Interfaces
14 interfaces between chains.
- A–B · 2840 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2645 Ų buried · 35 hydrogen bonds · protein-protein
- T–P · 874 Ų buried · 92 hydrogen bonds · nucleic-nucleic
- E–F · 853 Ų buried · 77 hydrogen bonds · nucleic-nucleic
- C–E · 774 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 4PWD · Crystal structure of HIV-1 reverse transcriptase in complex with bulge-RNA/DNA and… · 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 4PWD · PDBe 4PWD · UniProt P03366
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