MolNFT v1 · #135335 · protein

Crystal structure of HIV-1 reverse transcriptase in complex with 5-(2- (2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-YL)ETHOXY)-4-fluorophenoxy)- 7-fluoro-2-naphthonitrile (JLJ636), a non-nucleoside inhibitor

5TW3 · HIV-1 reverse transcriptase, P66 subunit: “Crystal structure of HIV-1 reverse transcriptase in complex with 5-(2…”. X-ray diffraction, 2 ligands (7N1, MG), 15 pockets (best druggability 0.75). MolNFT v1 #135335 on GenesisL1: 3D…

PDB: 5TW3
Type: protein
Length: 957 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 reverse transcriptase, P66 subunit; HIV-1 reverse transcriptase, P51 subunit
EC: 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
UniProt: P03366
Ligands: 7N1, MG
Pockets: 15 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HIV-1 reverse transcriptase, P66 subunit (EC 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2)	protein	548	32% helix, 24% strand	P03366
B	HIV-1 reverse transcriptase, P51 subunit (EC 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2)	protein	409	34% helix, 19% strand	P03366

Ligands and binding sites

7N1 · 5-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl) ethoxy]-4-fluorophenoxy}-7-fluoronaphthalene-2-carbonitrile · ligand · chains A
MG · Magnesium ion · metal · chains A

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	749	0.75	0.80	74	7N1
2	820	0.75	0.79	88	empty
3	285	0.66	0.82	37	empty
4	298	0.66	0.82	35	empty
5	433	0.64	0.77	44	empty

Interfaces

1 interface between chains.

A–B · 2598 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

5TW3 · Crystal Structure of HIV-1 Reverse Transcriptase 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 5TW3 · PDBe 5TW3 · UniProt P03366

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