MolNFT v1 · #72540 · protein

HIV-1 reverse transcriptase with aminopyrimidine inhibitor 2

3NBP · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “HIV-1 reverse transcriptase with aminopyrimidine inhibitor 2”. X-ray diffraction, 2 ligands (JGZ, MN), 14 pockets (best druggability 0.78). MolNFT v1 #72540 on GenesisL1: 3D structure, binding…

PDB: 3NBP
Type: protein
Length: 954 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
UniProt: P04585
Ligands: JGZ, MN
Pockets: 14 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 35% 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	554	32% helix, 23% strand	P04585
B	P51 rt	protein	400	38% helix, 18% strand	P04585

Ligands and binding sites

JGZ · 4-(4-{[4-(4-cyano-2,6-dimethylphenoxy)pyrimidin-2-yl]amino}piperidin-1-yl)benzenesulfonamide · ligand · chains A, B
MN · Manganese (II) ion · metal · 2 copies · chains A

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

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	822	0.78	0.81	78	JGZ
2	433	0.70	0.81	38	empty
3	261	0.67	0.83	37	empty
4	260	0.61	0.80	31	empty
5	229	0.55	0.78	29	empty

Interfaces

1 interface between chains.

A–B · 2855 Å² buried · 34 hydrogen bonds · protein-protein

Compared structures

3NBP · HIV-1 reverse transcriptase with aminopyrimidine inhibitor 2 · 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
Elsewhere: RCSB PDB 3NBP · PDBe 3NBP · UniProt P04585

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