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Crystal structure of the complex of pf-3450074 with an engineered HIV capsid N terminal domain

Analyse Crystal structure of the complex of pf-3450074 with an engineered HIV capsid N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2XDE
Type: protein
Length: 272 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gag polyprotein
UniProt: Q9IQV5
Ligands: 1B0
Pockets: 3 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 63% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Gag polyprotein	protein	136	63% helix, 4% strand	Q9IQV5

Ligands and binding sites

1B0 · N-methyl-nalpha-[(2-methyl-1H-indol-3-yl)acetyl]-N-phenyl-L-phenylalaninamide · ligand · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	333	0.57	0.76	38	1B0
2	86	0.37	0.76	13	1B0
3	83	0.35	0.76	19	empty

Interfaces

1 interface between chains.

A–B · 451 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2XDE · Crystal structure of the complex of PF-3450074 with an engineered HIV capsid N terminal… · 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 Q9IQV5
Elsewhere: RCSB PDB 2XDE · PDBe 2XDE · UniProt Q9IQV5

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