MolNFT v1 · #55537 · protein
HIV-1 reverse transcriptase Y188L mutant in complex with inhibitor GSK560
2YNF · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “HIV-1 reverse transcriptase Y188L mutant in complex with inhibitor GSK560”. X-ray diffraction, 2 ligands (WHU, MG), 17 pockets (best druggability 0.74). MolNFT v1 #55537 on GenesisL1: 3D…
- PDB
- 2YNF
- Type
- protein
- Length
- 963 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, 3.1.13.2
- UniProt
- P04585
- Ligands
- WHU, MG
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 36% 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, 3.1.26.13, 3.1.13.2) | protein | 557 | 34% helix, 23% strand | P04585 |
| B | P51 rt | protein | 406 | 39% helix, 19% strand | P04585 |
Ligands and binding sites
- WHU · 2-azanyl-N-[[4-bromanyl-3-(3-chloranyl-5-cyano-phenoxy)-2-fluoranyl-phenyl]methyl]-4-chloranyl-1H-imidazole-5-carboxamide · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- TAR · D(-)-tartaric acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.74 | 0.90 | 28 | WHU |
| 2 | 635 | 0.72 | 0.80 | 59 | empty |
| 3 | 273 | 0.67 | 0.83 | 41 | empty |
| 4 | 368 | 0.65 | 0.79 | 32 | empty |
| 5 | 354 | 0.63 | 0.79 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 2828 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 2YNF · HIV-1 Reverse Transcriptase Y188L mutant in complex with inhibitor GSK560 · 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 2YNF · PDBe 2YNF · UniProt P04585
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