MolNFT v1 · #163492 · protein

Structure of human KCTD1

6S4L · BTB/POZ domain-containing protein KCTD1: “Structure of human KCTD1”. X-ray diffraction, 2 ligands (NA, IOD), 17 pockets (best druggability 0.72). MolNFT v1 #163492 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6S4L
Type: protein
Length: 1,060 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BTB/POZ domain-containing protein KCTD1
UniProt: Q719H9
Ligands: NA, IOD
Pockets: 17 · best druggability 0.72

Structure

x-ray diffraction · 5 distinct chains · 32% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BTB/POZ domain-containing protein KCTD1	protein	217	31% helix, 28% strand	Q719H9
B	BTB/POZ domain-containing protein KCTD1	protein	211	33% helix, 25% strand	Q719H9
C	BTB/POZ domain-containing protein KCTD1	protein	212	33% helix, 26% strand	Q719H9
D	BTB/POZ domain-containing protein KCTD1	protein	215	31% helix, 26% strand	Q719H9
E	BTB/POZ domain-containing protein KCTD1	protein	205	32% helix, 27% strand	Q719H9

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains A, B, C, D, E
IOD · Iodide ion · ion · 2 copies · chains A, B, C, D, E

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

Pockets

17 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	843	0.72	0.77	93	empty
2	676	0.65	0.75	37	empty
3	390	0.57	0.75	36	NA
4	335	0.53	0.73	31	empty
5	129	0.43	0.76	18	empty

Interfaces

10 interfaces between chains.

A–E · 2103 Å² buried · 32 hydrogen bonds · protein-protein
C–D · 2103 Å² buried · 37 hydrogen bonds · protein-protein
B–C · 2092 Å² buried · 32 hydrogen bonds · protein-protein
D–E · 2045 Å² buried · 34 hydrogen bonds · protein-protein
A–B · 1927 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

6S4L · Structure of human KCTD1 · the same entry in another collection · chain E against E, 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 0.98

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 6S4L · PDBe 6S4L · UniProt Q719H9

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