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Crystal structure of HIV-1 reverse transcriptase in complex with dmp- 266(EFAVIRENZ)
Analyse Crystal structure of HIV-1 reverse transcriptase in complex with dmp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FK9
- Type
- protein
- Length
- 923 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
- 13 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 rt, a-chain (EC 2.7.7.49) | protein | 520 | 33% helix, 22% strand | P04585 |
| B | HIV-1 rt, B-chain (EC 2.7.7.49) | protein | 403 | 35% helix, 20% 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, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1141 | 0.79 | 0.80 | 110 | EFZ |
| 2 | 672 | 0.72 | 0.79 | 63 | empty |
| 3 | 461 | 0.65 | 0.78 | 40 | empty |
| 4 | 93 | 0.60 | 0.88 | 21 | empty |
| 5 | 183 | 0.52 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2506 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 1FK9 · Crystal structure of HIV-1 reverse transcriptase in complex with dmp-266(EFAVIRENZ) · 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 1FK9 · PDBe 1FK9 · UniProt P04585
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