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Apo HIV protease (pr) dimer in closed form with fragment 1F1 in the OUTSIDE/TOP of flap

Analyse Apo HIV protease (pr) dimer in closed form with fragment 1F1 in the OUTSIDE/TOP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4EJ8
Type: protein
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protease
EC: 3.4.23.16
UniProt: P12499
Ligands: 1F1
Pockets: 1 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protease (EC 3.4.23.16)	protein	99	4% helix, 56% strand	P12499

Ligands and binding sites

1F1 · 1H-indole-6-carboxylic acid · ligand · chains A
DMS · Dimethyl sulfoxide · additive · 5 copies · chains A, B
EDO · 1,2-ethanediol · additive · 4 copies · 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	490	0.66	0.78	39	DMS

Interfaces

1 interface between chains.

A–B · 1645 Å² buried · 34 hydrogen bonds · protein-protein

Compared structures

4EJ8 · Apo HIV Protease (PR) dimer in closed form with fragment 1F1 in the outside/top of flap · 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 P12499
Elsewhere: RCSB PDB 4EJ8 · PDBe 4EJ8 · UniProt P12499

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