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Co-crystal structure of human spop math domain (E47K) and human BRD3 fragment

Analyse Co-crystal structure of human spop math domain (E47K) and human BRD3 fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6I5P
Type: protein
Length: 579 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Speckle-type poz protein; Bromodomain-containing protein 3
UniProt: O43791, Q15059
Pockets: 4 · best druggability 0.51

Structure

x-ray diffraction · 5 distinct chains · 11% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Speckle-type poz protein	protein	136	13% helix, 48% strand	O43791
B, F, H	Bromodomain-containing protein 3	protein	7	0% helix, 14% strand	Q15059
C, E	Speckle-type poz protein	protein	138	10% helix, 47% strand	O43791
D	Bromodomain-containing protein 3	protein	6	0% helix, 17% strand	Q15059
G	Speckle-type poz protein	protein	140	12% helix, 46% strand	O43791

Pockets

4 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	246	0.51	0.75	31	empty
2	219	0.49	0.75	25	empty
3	208	0.48	0.75	24	empty
4	56	0.26	0.74	14	empty

Interfaces

8 interfaces between chains.

A–E · 889 Å² buried · 12 hydrogen bonds · protein-protein
C–G · 864 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 391 Å² buried · 15 hydrogen bonds · protein-protein
G–H · 378 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 376 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

6I5P · Co-crystal structure of human SPOP MATH domain (E47K) and human BRD3 fragment · the same entry in another collection · chain H against H, TM-score 1.00
O43791 · AlphaFold monomer V2.0 prediction for speckle-type poz protein (O43791) · a predicted model of the same protein · chain A against A, TM-score 0.96
Q15059 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 3 (Q15059) · a predicted model of the same protein · chain D against A, TM-score 0.57

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 O43791
Every structure of UniProt Q15059
Elsewhere: RCSB PDB 6I5P · PDBe 6I5P · UniProt O43791 · UniProt Q15059

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