MolNFT v1 · #20895 · protein
High resolution structures of HIV-1 rt from four rt- inhibitor complexes
1RTH · HIV-1 reverse transcriptase: “High resolution structures of HIV-1 rt from four rt- inhibitor complexes”. X-ray diffraction, 1 ligand (U05), 15 pockets (best druggability 0.81). MolNFT v1 #20895 on GenesisL1: 3D structure, binding…
- PDB
- 1RTH
- Type
- protein
- Length
- 963 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 reverse transcriptase
- EC
- 2.7.7.49
- UniProt
- P04585
- Ligands
- U05
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 reverse transcriptase (EC 2.7.7.49) | protein | 543 | 31% helix, 25% strand | P04585 |
| B | HIV-1 reverse transcriptase (EC 2.7.7.49) | protein | 420 | 34% helix, 20% strand | P04585 |
Ligands and binding sites
- U05 · 6,11-dihydro-11-ethyl-6-methyl-9-nitro-5H-pyrido[2,3-b][1,5]benzodiazepin-5-one · ligand · 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 | 875 | 0.81 | 0.83 | 76 | U05 |
| 2 | 488 | 0.76 | 0.84 | 43 | empty |
| 3 | 943 | 0.73 | 0.77 | 81 | empty |
| 4 | 432 | 0.63 | 0.77 | 44 | empty |
| 5 | 91 | 0.60 | 0.88 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2615 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 1RTH · High resolution structures of HIV-1 rt from four rt-inhibitor complexes · 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 1RTH · PDBe 1RTH · UniProt P04585
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