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Crystal Structure of HIV-1 Reverse Transcriptase K103N/Y181C Variant in Complex with (E)-4-((4-((4-(2-cyanovinyl)-2,6-dimethylphenyl)amino)-6-(3-morpholinopropoxy)-1,3,5-triazin-2-yl)amino)benzonitrile (JLJ564)

Analyse Crystal Structure of HIV-1 Reverse Transcriptase K103N/Y181C Variant in Complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SO3
Type: protein
Length: 937 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.767
Source: Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Molecule: Reverse transcriptase/ribonuclease H; p51 RT
EC: 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
UniProt: P03366
Ligands: 9W3, MG
Pockets: 16 · best druggability 0.79

Structure

x-ray diffraction · resolution 2.767 · 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, 2.7.7.7, 3.1.26.13, 3.1.13.2)	protein	537	32% helix, 24% strand	P03366
B	p51 RT	protein	400	36% helix, 20% strand	P03366

Ligands and binding sites

9W3 · 4-[(4-{4-[(E)-2-cyanoethenyl]-2,6-dimethylanilino}-6-[3-(morpholin-4-yl)propoxy]-1,3,5-triazin-2-yl) amino]benzonitrile · ligand · chains A, B
MG · Magnesium ion · metal · 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, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	990	0.79	0.81	89	9W3
2	712	0.77	0.81	69	empty
3	238	0.62	0.81	30	empty
4	393	0.60	0.76	43	empty
5	338	0.59	0.77	48	empty

Interfaces

1 interface between chains.

A–B · 2564 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

7SO3 · Crystal structure of HIV-1 reverse transcriptase K103N/Y181C variant 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 7SO3 · PDBe 7SO3 · UniProt P03366

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