MolNFT v1 · #118821 · protein
Crystal structure of K103N/Y181C mutant HIV-1 reverse transcriptase (rt) in complex with IDX899
5FDL · P51 reverse transcriptase: “Crystal structure of K103N/Y181C mutant HIV-1 reverse transcriptase (rt) in complex with IDX899”. X-ray diffraction, 1 ligand (5DV), 14 pockets (best druggability 0.80). MolNFT v1 #118821 on GenesisL1: 3D…
- PDB
- 5FDL
- Type
- protein
- Length
- 946 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P51 reverse transcriptase; P66 reverse transcriptase
- EC
- 2.7.7.49
- UniProt
- P03366
- Ligands
- 5DV
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P51 reverse transcriptase (EC 2.7.7.49) | protein | 550 | 32% helix, 24% strand | P03366 |
| B | P66 reverse transcriptase (EC 2.7.7.49) | protein | 396 | 37% helix, 18% strand | P03366 |
Ligands and binding sites
- 5DV · methyl (R)-(2-carbamoyl-5-chloro-1H-indol-3-yl)[3-(2-cyanoethyl)-5-methylphenyl]phosphinate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.80 | 0.81 | 113 | 5DV |
| 2 | 526 | 0.72 | 0.80 | 46 | empty |
| 3 | 368 | 0.64 | 0.79 | 45 | empty |
| 4 | 154 | 0.55 | 0.81 | 31 | empty |
| 5 | 86 | 0.52 | 0.84 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2600 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5FDL · Crystal Structure of K103N/Y181C Mutant HIV-1 Reverse Transcriptase (RT) in Complex with… · the same entry in another collection · chain B against B, 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 5FDL · PDBe 5FDL · UniProt P03366
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