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Crystal structure of the KCTD16 BTB domain in complex with GABAB2 peptide

Analyse Crystal structure of the KCTD16 BTB domain in complex with GABAB2 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6M8R
Type: protein
Length: 1,036 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.2
Source: Homo sapiens
Molecule: BTB/POZ domain-containing protein KCTD16; Gamma-aminobutyric acid type B receptor subunit…
UniProt: Q68DU8, O75899
Ligands: MG
Pockets: 11 · best druggability 0.83

Structure

x-ray diffraction · resolution 3.2 · 11 distinct chains · 39% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	BTB/POZ domain-containing protein KCTD16	protein	100	40% helix, 16% strand	Q68DU8
H	BTB/POZ domain-containing protein KCTD16	protein	95	42% helix, 17% strand	Q68DU8
I	BTB/POZ domain-containing protein KCTD16	protein	100	37% helix, 16% strand	Q68DU8
J, C	BTB/POZ domain-containing protein KCTD16	protein	97	38% helix, 16% strand	Q68DU8
B	BTB/POZ domain-containing protein KCTD16	protein	96	42% helix, 17% strand	Q68DU8
D	BTB/POZ domain-containing protein KCTD16	protein	99	40% helix, 16% strand	Q68DU8
E	BTB/POZ domain-containing protein KCTD16	protein	96	42% helix, 17% strand	Q68DU8
A	BTB/POZ domain-containing protein KCTD16	protein	95	39% helix, 17% strand	Q68DU8
F	BTB/POZ domain-containing protein KCTD16	protein	96	40% helix, 17% strand	Q68DU8
K	Gamma-aminobutyric acid type B receptor subunit 2	protein	33	30% helix, 6% strand	O75899
L	Gamma-aminobutyric acid type B receptor subunit 2	protein	32	34% helix, 6% strand	O75899

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	893	0.83	0.85	82	empty
2	855	0.79	0.82	90	empty
3	248	0.63	0.81	35	empty
4	120	0.59	0.85	25	empty
5	228	0.50	0.75	28	empty

Interfaces

25 interfaces between chains.

D–E · 877 Å² buried · 24 hydrogen bonds · protein-protein
I–J · 864 Å² buried · 24 hydrogen bonds · protein-protein
G–F · 847 Å² buried · 25 hydrogen bonds · protein-protein
B–A · 815 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 813 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

6M8R · Crystal structure of the KCTD16 btb domain in complex with GABAB2 peptide · the same entry in another collection · chain L against L, 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 Q68DU8
Every structure of UniProt O75899
Elsewhere: RCSB PDB 6M8R · PDBe 6M8R · UniProt Q68DU8 · UniProt O75899

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