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Crystal structure of HIV-1 reverse transcriptase (rt) in complex with janssen-R165481
Analyse Crystal structure of HIV-1 reverse transcriptase (rt) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B5J
- Type
- protein
- Length
- 979 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse transcriptase P66 subunit; Reverse transcriptase P51 subunit
- EC
- 2.7.7.49
- UniProt
- P03366
- Ligands
- 3AC, MN
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse transcriptase P66 subunit (EC 2.7.7.49) | protein | 552 | 32% helix, 22% strand | P03366 |
| B | Reverse transcriptase P51 subunit (EC 2.7.7.49) | protein | 427 | 31% helix, 17% strand | P03366 |
Ligands and binding sites
- 3AC · (2E)-3-{3-[(5-ethyl-3-iodo-6-methyl-2-oxo-1,2-dihydropyridin-4-yl)oxy]phenyl}acrylonitrile · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.80 | 0.82 | 93 | 3AC |
| 2 | 856 | 0.73 | 0.78 | 72 | empty |
| 3 | 478 | 0.71 | 0.81 | 39 | empty |
| 4 | 429 | 0.69 | 0.80 | 53 | empty |
| 5 | 280 | 0.65 | 0.82 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 2611 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 2B5J · Crystal structure of HIV-1 reverse transcriptase (RT) in complex with JANSSEN-R165481 · 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 2B5J · PDBe 2B5J · UniProt P03366
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