MolNFT v1 · #76550 · protein

Crystal structure of HIV-1 reverse transcriptase (rt) in complex with tsao-T, a non-nucleoside rt inhibitor (nnrti)

3QO9 · Reverse transcriptase/ ribonuclease H: “Crystal structure of HIV-1 reverse transcriptase (rt) in complex with tsao-T, a non-nucleoside rt inhibitor…”. X-ray diffraction, 1 ligand (QO9), 14 pockets (best druggability 0.83). MolNFT v1…

PDB: 3QO9
Type: protein
Length: 965 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Reverse transcriptase/ ribonuclease H; P51 rt
EC: 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.26.4
UniProt: P03366
Ligands: QO9
Pockets: 14 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 21% 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)	protein	553	33% helix, 23% strand	P03366
B	P51 rt (EC 2.7.7.7, 3.1.26.4)	protein	412	34% helix, 19% strand	P03366

Ligands and binding sites

QO9 · 1-[(5R,6R,8R,9R)-4-amino-9-{[tert-butyl(dimethyl)silyl]oxy}-6-({[tert-butyl(dimethyl)silyl]oxy}methyl)-2,2-dioxido-1,7-dioxa-2-thiaspiro[4.4]non-3-en-8-yl]-5-methylpyrimidine-2,4(1H,3H)-dione · ligand · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1091	0.83	0.83	89	QO9
2	591	0.76	0.82	68	empty
3	492	0.74	0.82	47	empty
4	447	0.68	0.79	71	empty
5	625	0.67	0.76	48	empty

Interfaces

1 interface between chains.

A–B · 2758 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

3QO9 · Crystal structure of HIV-1 Reverse Transcriptase (RT) in complex with TSAO-T, a… · 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 3QO9 · PDBe 3QO9 · UniProt P03366

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