MolNFT v1 · #154737 · protein

Human KCC1 structure determined in nacl and gdn

6KKU · Solute carrier family 12 member 4: “Human KCC1 structure determined in nacl and gdn”. Electron microscopy, 5 ligands (DU0, NAG, BGC), 14 pockets (best druggability 0.77). MolNFT v1 #154737 on GenesisL1: 3D structure, binding sites…

PDB: 6KKU
Type: protein
Length: 1,074 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Solute carrier family 12 member 4
UniProt: Q9UP95
Ligands: DU0, NAG, BGC, GLC, CL
Pockets: 14 · best druggability 0.77

Structure

electron microscopy · 1 distinct chain · 61% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Solute carrier family 12 member 4	protein	537	61% helix, 5% strand	Q9UP95

Ligands and binding sites

DU0 · 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R}, 9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4, 8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B

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

Pockets

14 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	819	0.77	0.81	89	empty
2	463	0.73	0.82	55	CL
3	461	0.71	0.81	50	empty
4	671	0.71	0.77	73	BGC, DU0
5	197	0.46	0.73	25	empty

Interfaces

1 interface between chains.

A–B · 1468 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

6KKU · human KCC1 structure determined in NaCl and GDN · the same entry in another collection · chain A against A, TM-score 1.00
Q9UP95 · AlphaFold monomer V2.0 prediction for solute carrier family 12 member 4 (Q9UP95) · 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 Q9UP95
Elsewhere: RCSB PDB 6KKU · PDBe 6KKU · UniProt Q9UP95

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