MolNFT v1 · #114689 · protein

Crystal structure of pentameric KCTD1 btb domain form 1

5BXB · BTB/POZ domain-containing protein KCTD1: “Crystal structure of pentameric KCTD1 btb domain form 1”. X-ray diffraction, 18 pockets (best druggability 0.74). MolNFT v1 #114689 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5BXB
Type: protein
Length: 1,059 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BTB/POZ domain-containing protein KCTD1
UniProt: Q719H9
Pockets: 18 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 39% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, J	BTB/POZ domain-containing protein KCTD1	protein	105	38% helix, 18% strand	Q719H9
C, F, G	BTB/POZ domain-containing protein KCTD1	protein	106	39% helix, 16% strand	Q719H9
D, H, I	BTB/POZ domain-containing protein KCTD1	protein	107	40% helix, 16% strand	Q719H9
E	BTB/POZ domain-containing protein KCTD1	protein	105	39% helix, 16% strand	Q719H9

Pockets

18 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	1190	0.74	0.77	90	empty
2	261	0.73	0.87	34	empty
3	681	0.69	0.77	88	empty
4	282	0.54	0.76	33	empty
5	127	0.48	0.79	18	empty

Interfaces

12 interfaces between chains.

F–G · 901 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 891 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 874 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 867 Å² buried · 21 hydrogen bonds · protein-protein
I–J · 865 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

5BXB · Crystal structure of pentameric KCTD1 BTB domain form 1 · the same entry in another collection · chain J against J, TM-score 1.00
Q719H9 · AlphaFold monomer V2.0 prediction for BTB/POZ domain-containing protein KCTD1 (Q719H9) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q719H9
Elsewhere: RCSB PDB 5BXB · PDBe 5BXB · UniProt Q719H9

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