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Crystal structure of aphrodisin, a sex pheromone from female hamster

Analyse Crystal structure of aphrodisin, a sex pheromone from female hamster in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1E5P
Type: protein
Length: 593 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aphrodisin
UniProt: P09465
Pockets: 5 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Aphrodisin	protein	149	17% helix, 49% strand	P09465
B	Aphrodisin	protein	148	15% helix, 49% strand	P09465
C	Aphrodisin	protein	147	15% helix, 49% strand	P09465

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	123	0.82	0.98	18	empty
2	112	0.81	0.98	19	empty
3	95	0.80	0.99	15	empty
4	76	0.76	0.98	17	empty
5	120	0.39	0.74	24	empty

Interfaces

4 interfaces between chains.

B–D · 530 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 517 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 293 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 134 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified, 8 disulfide (engineered, disulfide).

Compared structures

1E5P · Crystal structure of aphrodisin, a sex pheromone from female hamster · the same entry in another collection · chain D against D, TM-score 1.00
P09465 · AlphaFold monomer V2.0 prediction for aphrodisin (P09465) · a predicted model of the same protein · chain D 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 P09465
Elsewhere: RCSB PDB 1E5P · PDBe 1E5P · UniProt P09465

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