Research workbench
Crystal structure of HIV-1 rt bound to a 6-vinylpyrimidine inhibitor
Analyse Crystal structure of HIV-1 rt bound to a 6-vinylpyrimidine inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ISN
- Type
- protein
- Length
- 971 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
- EDM
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 556 | 31% helix, 22% strand | P03366 |
| D | P51 rt | protein | 415 | 35% helix, 20% strand | P03366 |
Ligands and binding sites
- EDM · 6-ethenyl-N,N-dimethyl-2-(methylsulfonyl)pyrimidin-4-amine · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.76 | 0.78 | 74 | empty |
| 2 | 599 | 0.69 | 0.78 | 62 | empty |
| 3 | 350 | 0.64 | 0.79 | 38 | empty |
| 4 | 305 | 0.62 | 0.79 | 46 | empty |
| 5 | 169 | 0.58 | 0.82 | 20 | empty |
Interfaces
1 interface between chains.
- C–D · 2726 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3ISN · Crystal structure of HIV-1 RT bound to A 6-vinylpyrimidine inhibitor · the same entry in another collection · chain C against C, 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 3ISN · PDBe 3ISN · UniProt P03366
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