MolNFT v1 · #92246 · protein
Crystal structure of HIV-1 reverse transcriptase (rt) in complex with rilpivirine (TMC278, edurant), a non-nucleoside rt-inhibiting drug
4G1Q · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “Crystal structure of HIV-1 reverse transcriptase (rt) in complex with rilpivirine (TMC278, edurant), a…”. X-ray diffraction, 3 ligands (T27, MG, SO4), 15 pockets (best druggability 0.77).…
- PDB
- 4G1Q
- Type
- protein
- Length
- 972 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, 3.1.26.13
- UniProt
- P03366
- Ligands
- T27, MG, SO4
- Pockets
- 15 · best druggability 0.77
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, 3.1.26.13) | protein | 556 | 33% helix, 23% strand | P03366 |
| B | P51 rt (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 416 | 36% helix, 19% strand | P03366 |
Ligands and binding sites
- T27 · 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile · ligand · chains A, B
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.77 | 0.81 | 89 | EDO |
| 2 | 289 | 0.75 | 0.87 | 40 | T27, EDO |
| 3 | 519 | 0.75 | 0.82 | 44 | SO4 |
| 4 | 661 | 0.71 | 0.78 | 50 | empty |
| 5 | 257 | 0.67 | 0.84 | 33 | SO4, EDO |
Interfaces
1 interface between chains.
- A–B · 2711 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 4G1Q · Crystal structure of HIV-1 reverse transcriptase (RT) in complex with Rilpivirine… · 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 4G1Q · PDBe 4G1Q · UniProt P03366
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