Research workbench
HIV-1 reverse transcriptase with inhibitor
Analyse HIV-1 reverse transcriptase with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LP1
- Type
- protein
- Length
- 954 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; P51 rt
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.4
- UniProt
- P04585
- Ligands
- LP8, NVP, MN
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 554 | 32% helix, 22% strand | P04585 |
| B | P51 rt (EC 2.7.7.49, 2.7.7.7) | protein | 400 | 36% helix, 20% strand | P04585 |
Ligands and binding sites
- LP8 · 3-cyclopentyl-1,4-dihydroxy-1,8-naphthyridin-2(1H)-one · ligand · chains A
- NVP · 11-cyclopropyl-5,11-dihydro-4-methyl-6H-dipyrido[3,2-B:2',3'-e][1,4]diazepin-6-one · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 834 | 0.79 | 0.82 | 72 | NVP |
| 2 | 720 | 0.74 | 0.80 | 69 | empty |
| 3 | 258 | 0.66 | 0.83 | 37 | empty |
| 4 | 66 | 0.56 | 0.88 | 16 | empty |
| 5 | 180 | 0.53 | 0.78 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2757 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3LP1 · HIV-1 reverse transcriptase with inhibitor · 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 3LP1 · PDBe 3LP1 · UniProt P04585
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