Research workbench
HIV-1 reverse transcriptase complexed with 4-iodopyrazole
Analyse HIV-1 reverse transcriptase complexed with 4-iodopyrazole in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CYM
- Type
- protein
- Length
- 954 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 reverse transcriptase, P66 subunit; HIV-1 reverse transcriptase, P51 subunit
- EC
- 2.7.7.49
- UniProt
- P03366
- Ligands
- PYZ, T27, IOD, SO4
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 reverse transcriptase, P66 subunit (EC 2.7.7.49) | protein | 546 | 32% helix, 23% strand | P03366 |
| B | HIV-1 reverse transcriptase, P51 subunit (EC 2.7.7.49) | protein | 408 | 36% helix, 20% strand | P03366 |
Ligands and binding sites
- PYZ · 4-iodopyrazole · ligand · 6 copies · chains A, B
- T27 · 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile · ligand · chains A, B
- IOD · Iodide ion · ion · 14 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.82 | 0.83 | 108 | T27, EDO, PYZ, DMS |
| 2 | 504 | 0.74 | 0.82 | 45 | SO4, PYZ |
| 3 | 291 | 0.65 | 0.81 | 39 | PYZ |
| 4 | 405 | 0.60 | 0.76 | 41 | PYZ |
| 5 | 274 | 0.59 | 0.78 | 35 | DMS |
Interfaces
1 interface between chains.
- A–B · 2625 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5CYM · HIV-1 reverse transcriptase complexed with 4-iodopyrazole · 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 5CYM · PDBe 5CYM · UniProt P03366
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