MolNFT v1 · #98357 · protein

CA2+-bound E212Q mutant mthk rck domain

4L76 · Calcium-gated potassium channel mthk: “CA2+-bound E212Q mutant mthk rck domain”. X-ray diffraction, 2 ligands (CA, NA), 20 pockets (best druggability 0.81). MolNFT v1 #98357 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4L76
Type: protein
Length: 1,340 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Calcium-gated potassium channel mthk
UniProt: O27564
Ligands: CA, NA
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 6 distinct chains · 36% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Calcium-gated potassium channel mthk	protein	227	35% helix, 22% strand	O27564
B	Calcium-gated potassium channel mthk	protein	224	36% helix, 22% strand	O27564
C	Calcium-gated potassium channel mthk	protein	221	36% helix, 23% strand	O27564
D	Calcium-gated potassium channel mthk	protein	222	35% helix, 25% strand	O27564
E	Calcium-gated potassium channel mthk	protein	223	37% helix, 23% strand	O27564
F	Calcium-gated potassium channel mthk	protein	223	36% helix, 24% strand	O27564

Ligands and binding sites

CA · Calcium ion · metal · 13 copies · chains A, B, C, D, E, F
NA · Sodium ion · metal · 2 copies · chains B, D

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

Pockets

20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	866	0.81	0.83	86	empty
2	1194	0.77	0.79	67	empty
3	491	0.75	0.83	59	CA
4	339	0.72	0.85	43	CA
5	703	0.72	0.78	54	empty

Interfaces

11 interfaces between chains.

A–B · 3704 Å² buried · 45 hydrogen bonds · protein-protein
E–F · 3693 Å² buried · 46 hydrogen bonds · protein-protein
C–D · 3623 Å² buried · 49 hydrogen bonds · protein-protein
B–F · 654 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 644 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4L76 · Ca2+-bound E212Q mutant MthK RCK domain · the same entry in another collection · chain C against C, 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 O27564
Elsewhere: RCSB PDB 4L76 · PDBe 4L76 · UniProt O27564

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