MolNFT v1 · #146844 · protein
Crystal structure of HIV-1 reverse transcriptase V106A/F227L mutant in complex with non-nucleoside inhibitor 25A
6DUF · P66 rt: “Crystal structure of HIV-1 reverse transcriptase V106A/F227L mutant in complex with non-nucleoside inhibitor…”. X-ray diffraction, 3 ligands (K5C, MG, SO4), 18 pockets (best druggability 0.81). MolNFT v1 #146844 on…
- PDB
- 6DUF
- Type
- protein
- Length
- 968 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P66 rt; P51 rt
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13
- UniProt
- P03366
- Ligands
- K5C, MG, SO4
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P66 rt (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 556 | 32% helix, 24% strand | P03366 |
| B | P51 rt | protein | 412 | 33% helix, 19% strand | P03366 |
Ligands and binding sites
- K5C · 4-({4-[(4-{4-[(E)-2-cyanoethenyl]-2,6-dimethylphenoxy}thieno[3,2-d]pyrimidin-2-yl) amino]piperidin-1-yl}methyl)benzene-1-sulfonamide · ligand · chains A, B
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 9 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.81 | 0.82 | 94 | K5C, EDO |
| 2 | 514 | 0.75 | 0.83 | 43 | EDO, SO4 |
| 3 | 164 | 0.73 | 0.91 | 25 | empty |
| 4 | 635 | 0.69 | 0.77 | 46 | EDO |
| 5 | 253 | 0.56 | 0.77 | 39 | EDO, DMS |
Interfaces
1 interface between chains.
- A–B · 2705 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6DUF · Crystal structure of HIV-1 reverse transcriptase V106A/F227L mutant in complex with… · 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 6DUF · PDBe 6DUF · UniProt P03366
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