Research workbench

HIV-1 rt with nnrti tmc-125

Analyse HIV-1 rt with nnrti tmc-125 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3M8P
Type: protein
Length: 952 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, 3.1.26.4
UniProt: P04585
Ligands: 65B
Pockets: 16 · best druggability 0.79

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, 3.1.26.4)	protein	551	32% helix, 23% strand	P04585
B	P51 rt	protein	401	39% helix, 18% strand	P04585

Ligands and binding sites

65B · 4-({6-amino-5-bromo-2-[(4-cyanophenyl)amino]pyrimidin-4-yl}oxy)-3,5-dimethylbenzonitrile · ligand · chains A, B

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

Pockets

16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	723	0.79	0.83	66	65B
2	449	0.71	0.81	41	empty
3	296	0.68	0.83	39	empty
4	220	0.55	0.78	32	empty
5	249	0.52	0.75	40	empty

Interfaces

1 interface between chains.

A–B · 2825 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

3M8P · HIV-1 RT with NNRTI TMC-125 · the same entry in another collection · chain B against B, 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 3M8P · PDBe 3M8P · UniProt P04585

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