Research workbench
Crystal structure of HIV-1 reverse transcriptase (rt) in complex with the non-nucleoside rt inhibitor (E)-S-methyl 5-(1-(3,7-dimethyl-2- oxo-2,3-DIHYDROBENZO[D]OXAZOL-5-yl)-5-(5-methyl-1,3,4-oxadiazol-2- YL)PENT-1-enyl)-2-methoxy-3-methylbenzothioate.
Analyse Crystal structure of HIV-1 reverse transcriptase (rt) in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IRX
- Type
- protein
- Length
- 971 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; Reverse transcriptase
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.4
- UniProt
- P03366
- Ligands
- UDR
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 555 | 30% helix, 23% strand | P03366 |
| B | Reverse transcriptase (EC 2.7.7.49, 2.7.7.7) | protein | 416 | 32% helix, 19% strand | P03366 |
Ligands and binding sites
- UDR · (E)-S-Methyl 5-(1-(3,7-Dimethyl-2-oxo-2,3-dihydrobenzo[d]oxazol-5-yl)-5-(5-methyl-1,3,4-oxadiazol-2-yl)pent-1-enyl)-2-methoxy-3-methy lbenzothioate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.79 | 0.83 | 53 | empty |
| 2 | 483 | 0.76 | 0.84 | 58 | empty |
| 3 | 336 | 0.76 | 0.87 | 28 | UDR |
| 4 | 328 | 0.72 | 0.84 | 33 | empty |
| 5 | 610 | 0.69 | 0.77 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 2629 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3IRX · Crystal Structure of HIV-1 reverse transcriptase (RT) in complex with the Non-nucleoside… · 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 3IRX · PDBe 3IRX · UniProt P03366
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