MolNFT v1 · #76457 · protein
HIV-1 reverse transcriptase in complex with manicol at the RNase H active site and TMC278 (rilpivirine) at the nnrti binding pocket
3QLH · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “HIV-1 reverse transcriptase in complex with manicol at the RNase H active site and TMC278 (rilpivirine) at…”. X-ray diffraction, 3 ligands (MNK, T27, MN), 20 pockets (best druggability 0.79).…
- PDB
- 3QLH
- Type
- protein
- Length
- 962 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13
- UniProt
- P03366
- Ligands
- MNK, T27, MN
- Pockets
- 20 · 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, 3.1.26.13) | protein | 555 | 32% helix, 23% strand | P03366 |
| B | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7) | protein | 407 | 37% helix, 20% strand | P03366 |
Ligands and binding sites
- MNK · (2S)-5,7-dihydroxy-9-methyl-2-(prop-1-en-2-yl)-1,2,3,4-tetrahydro-6H-benzo[7]annulen-6-one · ligand · chains A
- T27 · 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile · ligand · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · chains B
- EDO · 1,2-ethanediol · additive · 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.79 | 0.82 | 73 | T27 |
| 2 | 614 | 0.75 | 0.81 | 51 | empty |
| 3 | 230 | 0.73 | 0.88 | 27 | DMS |
| 4 | 640 | 0.69 | 0.77 | 49 | empty |
| 5 | 184 | 0.60 | 0.83 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 2706 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 3QLH · HIV-1 Reverse Transcriptase in Complex with Manicol at the RNase H Active Site and TMC278… · 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 3QLH · PDBe 3QLH · UniProt P03366
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