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Crystal structure of human apolipoprotein D (apod) in complex with progesterone

Analyse Crystal structure of human apolipoprotein D (apod) in complex with progesterone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2HZQ
Type: protein
Length: 166 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apolipoprotein D
UniProt: P05090
Ligands: STR
Pockets: 1 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Apolipoprotein D	protein	166	10% helix, 43% strand	P05090

Ligands and binding sites

STR · Progesterone · ligand · chains A

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	333	0.67	0.81	33	STR

Modifications

Observed in the structure: 3 modified, 2 disulfide (engineered, disulfide).

Compared structures

2HZQ · Crystal structure of human apolipoprotein D (ApoD) in complex with progesterone · the same entry in another collection · chain A against A, TM-score 1.00
P05090 · AlphaFold monomer V2.0 prediction for apolipoprotein D (P05090) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P05090
Elsewhere: RCSB PDB 2HZQ · PDBe 2HZQ · UniProt P05090

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