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Crystal structure of HIV-1 reverse transcriptase (rt) in complex with TMC278 (rilpivirine), a non-nucleoside rt inhibitor
Analyse Crystal structure of HIV-1 reverse transcriptase (rt) in complex with TMC278… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZD1
- Type
- protein
- Length
- 966 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
- P03366
- Ligands
- T27, SO4
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 33% 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 | 554 | 31% helix, 24% strand | P03366 |
| B | P51 rt | protein | 412 | 35% helix, 20% 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
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.77 | 0.82 | 88 | empty |
| 2 | 586 | 0.77 | 0.83 | 47 | empty |
| 3 | 321 | 0.76 | 0.87 | 42 | T27 |
| 4 | 584 | 0.68 | 0.77 | 47 | empty |
| 5 | 94 | 0.67 | 0.92 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2662 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 2ZD1 · Crystal Structure of HIV-1 Reverse Transcriptase (RT) in Complex with 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 2ZD1 · PDBe 2ZD1 · UniProt P03366
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