Research workbench
Crystal structure of Y181C mutant HIV-1 reverse transcriptase in complex with tnk-651
Analyse Crystal structure of Y181C mutant HIV-1 reverse transcriptase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JLA
- Type
- protein
- Length
- 955 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 rt a-chain; HIV-1 rt B-chain
- EC
- 2.7.7.49
- UniProt
- P04585
- Ligands
- TNK
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 rt a-chain (EC 2.7.7.49) | protein | 547 | 32% helix, 24% strand | P04585 |
| B | HIV-1 rt B-chain (EC 2.7.7.49) | protein | 408 | 37% helix, 20% strand | P04585 |
Ligands and binding sites
- TNK · 6-benzyl-1-benzyloxymethyl-5-isopropyl uracil · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.80 | 0.81 | 97 | TNK |
| 2 | 534 | 0.76 | 0.83 | 39 | empty |
| 3 | 97 | 0.63 | 0.89 | 21 | empty |
| 4 | 349 | 0.57 | 0.76 | 43 | empty |
| 5 | 328 | 0.56 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 2778 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 1JLA · Crystal structure of Y181C mutant HIV-1 reverse transcriptase in complex with tnk-651 · 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 P04585
- Elsewhere: RCSB PDB 1JLA · PDBe 1JLA · UniProt P04585
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