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Crystal structure of HIV-1 E138K mutant reverse transcriptase in complex with non-nucleoside inhibitor 25A
Analyse Crystal structure of HIV-1 E138K mutant reverse transcriptase 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
- 6C0P
- Type
- protein
- Length
- 968 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; Reverse transcriptase P51 subunit
- EC
- 2.7.7.49
- UniProt
- P03366
- Ligands
- K5C, MG, SO4
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49) | protein | 556 | 33% helix, 24% strand | P03366 |
| B | Reverse transcriptase P51 subunit (EC 2.7.7.49) | protein | 412 | 35% 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 · 27 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
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.81 | 0.82 | 99 | K5C, SO4, EDO |
| 2 | 489 | 0.74 | 0.83 | 45 | EDO, SO4 |
| 3 | 708 | 0.69 | 0.77 | 54 | EDO |
| 4 | 217 | 0.68 | 0.86 | 35 | EDO |
| 5 | 296 | 0.58 | 0.77 | 40 | EDO, DMS |
Interfaces
1 interface between chains.
- A–B · 2702 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6C0P · Crystal structure of HIV-1 E138K mutant reverse transcriptase 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 6C0P · PDBe 6C0P · UniProt P03366
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