Research workbench
HIV-1 reverse transcriptase in complex with a 2,6-difluorophenyl dapy analog
Analyse HIV-1 reverse transcriptase in complex with a 2,6-difluorophenyl dapy analog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K14
- Type
- protein
- Length
- 937 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 reverse TRANSCRIPTASE(ISOLATE HXB2); HIV-1 reverse transcriptase (isolate LW123)
- EC
- 2.7.7.49
- UniProt
- P04585, P0C6F2
- Ligands
- IB1
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 reverse TRANSCRIPTASE(ISOLATE HXB2) | protein | 536 | 32% helix, 23% strand | P04585 |
| B | HIV-1 reverse transcriptase (isolate LW123) (EC 2.7.7.49) | protein | 401 | 37% helix, 19% strand | P0C6F2 |
Ligands and binding sites
- IB1 · 4-{[4-(2,6-difluoro-4-methoxybenzene-1-carbonyl) pyrimidin-2-yl]amino}benzonitrile · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 881 | 0.80 | 0.83 | 83 | IB1 |
| 2 | 530 | 0.69 | 0.78 | 48 | empty |
| 3 | 263 | 0.68 | 0.84 | 36 | empty |
| 4 | 205 | 0.55 | 0.78 | 33 | empty |
| 5 | 148 | 0.48 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2619 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5K14 · HIV-1 Reverse Transcriptase in complex with a 2,6-difluorophenyl DAPY analog · 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
- Every structure of UniProt P0C6F2
- Elsewhere: RCSB PDB 5K14 · PDBe 5K14 · UniProt P04585 · UniProt P0C6F2
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