Research workbench
HIV-1 reverse transcriptase with bound fragment near knuckles site
Analyse HIV-1 reverse transcriptase with bound fragment near knuckles site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IG3
- Type
- protein
- Length
- 972 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, 3.1.26.13
- UniProt
- P03366
- Ligands
- T27, J94
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 556 | 33% helix, 24% strand | P03366 |
| B | P51 rt (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 416 | 36% helix, 19% strand | P03366 |
Ligands and binding sites
- T27 · 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile · ligand · chains A, B
- J94 · (5S)-6,6-dimethyl-5-[(6R)-8-oxo-6,8-dihydrofuro[3,4-e][1,3]benzodioxol-6-yl]-5,6,7,8-tetrahydro[1, 3]dioxolo[4,5-g]isoquinolin-6-ium · ligand · chains A, B
- DMS · Dimethyl sulfoxide · additive · 15 copies · chains A, B
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 | 1110 | 0.80 | 0.81 | 103 | T27, J94, DMS |
| 2 | 552 | 0.74 | 0.81 | 41 | DMS |
| 3 | 137 | 0.72 | 0.92 | 22 | empty |
| 4 | 708 | 0.72 | 0.78 | 52 | empty |
| 5 | 305 | 0.58 | 0.77 | 44 | DMS |
Interfaces
1 interface between chains.
- A–B · 2750 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 4IG3 · HIV-1 reverse transcriptase with bound fragment near Knuckles site · 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 4IG3 · PDBe 4IG3 · UniProt P03366
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