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Structure of ebp and U18666A

Analyse Structure of ebp and U18666A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6OHT
Type: protein
Length: 618 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-beta-hydroxysteroid-DELTA(8),DELTA(7)-isomerase
EC: 5.3.3.5
UniProt: Q15125
Ligands: MKM
Pockets: 10 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 70% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	3-beta-hydroxysteroid-DELTA(8),DELTA(7)-isomerase (EC 5.3.3.5)	protein	206	70% helix, 0% strand	Q15125

Ligands and binding sites

MKM · 3beta-(2-Diethylaminoethoxy)androst-5-en-17-one · ligand · 3 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	448	0.78	0.86	39	MKM
2	423	0.76	0.84	38	MKM
3	440	0.76	0.84	40	MKM
4	128	0.44	0.75	17	empty
5	116	0.43	0.75	18	empty

Interfaces

1 interface between chains.

A–B · 1640 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (engineered).

Compared structures

6OHT · Structure of EBP and U18666A · the same entry in another collection · chain A against A, TM-score 1.00
Q15125 · AlphaFold monomer V2.0 prediction for 3-beta-hydroxysteroid- DELTA(8),DELTA(7)-isomerase… · a predicted model of the same protein · chain C against A, TM-score 0.97

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 Q15125
Elsewhere: RCSB PDB 6OHT · PDBe 6OHT · UniProt Q15125

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