Research workbench
Crystal structure of HIV-1 reverse transcriptase in complex with tnk- 6123
Analyse Crystal structure of HIV-1 reverse transcriptase in complex with tnk- 6123 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1C1C
- Type
- protein
- Length
- 953 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 reverse transcriptase (a-chain); HIV-1 reverse transcriptase (B-chain)
- EC
- 2.7.7.49
- UniProt
- P04585
- Ligands
- 612
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 reverse transcriptase (a-chain) (EC 2.7.7.49) | protein | 537 | 31% helix, 23% strand | P04585 |
| B | HIV-1 reverse transcriptase (B-chain) (EC 2.7.7.49) | protein | 416 | 34% helix, 20% strand | P04585 |
Ligands and binding sites
- 612 · 6-(cyclohexylsulfanyl)-1-(ethoxymethyl)-5-(1-methylethyl)pyrimidine-2,4(1H,3H)-dione · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.80 | 0.81 | 86 | 612 |
| 2 | 582 | 0.75 | 0.82 | 49 | empty |
| 3 | 443 | 0.67 | 0.79 | 40 | empty |
| 4 | 244 | 0.62 | 0.81 | 27 | empty |
| 5 | 93 | 0.60 | 0.87 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2563 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 1C1C · Crystal structure of HIV-1 reverse transcriptase in complex with tnk-6123 · 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 1C1C · PDBe 1C1C · UniProt P04585
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