Research workbench
Crystal structure of the HIV-1 reverse transcriptase bound to a 6-vinylpyrimidine inhibitor
Analyse Crystal structure of the HIV-1 reverse transcriptase bound to a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ITH
- Type
- protein
- Length
- 1,942 residues
- Chains
- 4
- 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
- EDM
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 556 | 28% helix, 20% strand | P03366 |
| B, D | P51 rt | protein | 415 | 32% helix, 16% strand | P03366 |
Ligands and binding sites
- EDM · 6-ethenyl-N,N-dimethyl-2-(methylsulfonyl)pyrimidin-4-amine · ligand · 2 copies · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.74 | 0.79 | 71 | empty |
| 2 | 687 | 0.73 | 0.79 | 48 | empty |
| 3 | 427 | 0.72 | 0.83 | 57 | empty |
| 4 | 611 | 0.68 | 0.77 | 71 | empty |
| 5 | 536 | 0.66 | 0.77 | 55 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2841 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2813 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 35 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3ITH · Crystal structure of the HIV-1 reverse transcriptase bound to a 6-vinylpyrimidine… · 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 3ITH · PDBe 3ITH · UniProt P03366
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