Research workbench
Crystal structure of HIV-1 rt in complex with nbd-14075
Analyse Crystal structure of HIV-1 rt in complex with nbd-14075 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LQU
- Type
- protein
- Length
- 968 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse transcriptase P66; Reverse transcriptase P51
- EC
- 2.7.7.49
- UniProt
- P03366
- Ligands
- YBD, SO4
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse transcriptase P66 (EC 2.7.7.49) | protein | 556 | 28% helix, 24% strand | P03366 |
| B | Reverse transcriptase P51 | protein | 412 | 34% helix, 19% strand | P03366 |
Ligands and binding sites
- YBD · ~{N}-[(1~{R})-2-azanyl-1-[5-(hydroxymethyl)-1,3-thiazol-2-yl]ethyl]-5-(4-chloranyl-3-fluoranyl-phenyl)-1~{H}-pyrrole-2-carboxamide · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 675 | 0.76 | 0.81 | 64 | empty |
| 2 | 657 | 0.76 | 0.81 | 65 | empty |
| 3 | 325 | 0.73 | 0.85 | 46 | YBD |
| 4 | 536 | 0.70 | 0.79 | 78 | empty |
| 5 | 512 | 0.68 | 0.79 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 2800 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 7LQU · Crystal Structure of HIV-1 RT in Complex with NBD-14075 · 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 7LQU · PDBe 7LQU · UniProt P03366
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