MolNFT v1 · #115471 · protein

Crystal structure of LEGK4_AMPPNP kinase

5CKW: “Crystal structure of LEGK4_AMPPNP kinase”. X-ray diffraction, 3 ligands (ANP, MG, CA), 9 pockets (best druggability 0.66). MolNFT v1 #115471 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5CKW
Type: protein
Length: 778 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: LEGK4
UniProt: Q5WZW9
Ligands: ANP, MG, CA
Pockets: 9 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	LEGK4	protein	400	51% helix, 15% strand	Q5WZW9
A	LEGK4	protein	378	47% helix, 15% strand	Q5WZW9

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains B, A
MG · Magnesium ion · metal · 4 copies · chains B, A
CA · Calcium ion · metal · 2 copies · chains B, A

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

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	223	0.66	0.84	19	empty
2	283	0.61	0.79	38	ANP, MG
3	268	0.60	0.79	36	ANP, MG
4	83	0.49	0.82	18	empty
5	146	0.44	0.75	22	empty

Interfaces

1 interface between chains.

B–A · 936 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

5CKW · Crystal structure of LegK4_AMPPNP Kinase · the same entry in another collection · chain B against B, 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 Q5WZW9
Elsewhere: RCSB PDB 5CKW · PDBe 5CKW · UniProt Q5WZW9

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