MolNFT v1 · #70590 · protein
HIV-1 reverse transcriptase with inhibitor
3LP0 · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “HIV-1 reverse transcriptase with inhibitor”. X-ray diffraction, 3 ligands (LP7, NVP, MN), 16 pockets (best druggability 0.79). MolNFT v1 #70590 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3LP0
- Type
- protein
- Length
- 955 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
- LP7, NVP, MN
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 22% 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 | 555 | 32% helix, 24% strand | P04585 |
| B | P51 rt (EC 2.7.7.49, 2.7.7.7) | protein | 400 | 37% helix, 19% strand | P04585 |
Ligands and binding sites
- LP7 · ethyl 1,4-dihydroxy-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxylate · 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
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.79 | 0.83 | 69 | NVP |
| 2 | 681 | 0.74 | 0.80 | 68 | empty |
| 3 | 276 | 0.64 | 0.81 | 36 | empty |
| 4 | 108 | 0.54 | 0.83 | 21 | empty |
| 5 | 193 | 0.49 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2841 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3LP0 · 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 3LP0 · PDBe 3LP0 · UniProt P04585
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