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Crystal structure of nnrti resistant K103N mutant HIV-1 reverse transcriptase in complex with dmp-266(EFAVIRENZ)
Analyse Crystal structure of nnrti resistant K103N mutant HIV-1 reverse transcriptase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FKO
- Type
- protein
- Length
- 946 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 rt, a-chain; HIV-1 rt, B-chain
- EC
- 2.7.7.49
- UniProt
- P04585
- Ligands
- EFZ
- Pockets
- 16 · 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 rt, a-chain (EC 2.7.7.49) | protein | 543 | 31% helix, 25% strand | P04585 |
| B | HIV-1 rt, B-chain (EC 2.7.7.49) | protein | 403 | 35% helix, 21% strand | P04585 |
Ligands and binding sites
- EFZ · (-)-6-chloro-4-cyclopropylethynyl-4-trifluoromethyl-1, 4-dihydro-2H-3,1-benzoxazin-2-one · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.81 | 0.82 | 94 | EFZ |
| 2 | 635 | 0.73 | 0.80 | 55 | empty |
| 3 | 426 | 0.63 | 0.77 | 40 | empty |
| 4 | 409 | 0.63 | 0.77 | 41 | empty |
| 5 | 85 | 0.58 | 0.87 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2731 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 1FKO · Crystal structure of nnrti resistant K103N mutant HIV-1 reverse transcriptase in complex… · 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 1FKO · PDBe 1FKO · UniProt P04585
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