Research workbench
Crystal structure of HIV-1 reverse transcriptase (rt) in complex with a triazole derived nnrti
Analyse Crystal structure of HIV-1 reverse transcriptase (rt) in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RKI
- Type
- protein
- Length
- 959 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 reverse transcriptase (rt) P66; HIV-1 reverse transcriptase (rt) P51
- EC
- 2.7.7.49
- UniProt
- P04585
- Ligands
- TT1, MG, SO4, CL
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 reverse transcriptase (rt) P66 (EC 2.7.7.49) | protein | 557 | 32% helix, 23% strand | P04585 |
| B | HIV-1 reverse transcriptase (rt) P51 (EC 2.7.7.49) | protein | 402 | 38% helix, 20% strand | P04585 |
Ligands and binding sites
- TT1 · 4-benzyl-3-[(2-chlorobenzyl)sulfanyl]-5-thiophen-2-yl-4H-1,2,4-triazole · ligand · chains A, B
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.81 | 0.82 | 111 | TT1 |
| 2 | 451 | 0.72 | 0.82 | 37 | empty |
| 3 | 279 | 0.68 | 0.83 | 32 | empty |
| 4 | 189 | 0.54 | 0.79 | 30 | empty |
| 5 | 208 | 0.49 | 0.75 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 2786 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 2RKI · Crystal Structure of HIV-1 Reverse Transcriptase (RT) in Complex with a triazole derived… · 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 2RKI · PDBe 2RKI · UniProt P04585
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