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Comparing the accumulation of active site and non-active site mutations in the HIV-1 protease

Analyse Comparing the accumulation of active site and non-active site mutations in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1SGU
Type: protein
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pol polyprotein
EC: 3.4.23.16
UniProt: P03367
Ligands: MK1
Pockets: 1 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pol polyprotein (EC 3.4.23.16)	protein	99	4% helix, 54% strand	P03367

Ligands and binding sites

MK1 · N-[2(R)-hydroxy-1(S)-indanyl]-5-[(2(S)-tertiary butylaminocarbonyl)-4(3-pyridylmethyl)piperazino]-4(S)-hydroxy-2(R)-phenylmethylpentanamide · ligand · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	377	0.71	0.83	35	MK1

Interfaces

1 interface between chains.

A–B · 1850 Å² buried · 36 hydrogen bonds · protein-protein

Compared structures

1SGU · Comparing the Accumulation of Active Site and Non-active Site Mutations in the HIV-1… · 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 P03367
Elsewhere: RCSB PDB 1SGU · PDBe 1SGU · UniProt P03367

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