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Crystal structure of the leucine zipper domain of cgmp dependent protein kinase I beta

Analyse Crystal structure of the leucine zipper domain of cgmp dependent protein kinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3NMD
Type: protein
Length: 254 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cgmp dependent protein kinase
UniProt: Q6P5T7
Pockets: 4 · best druggability 0.52

Structure

x-ray diffraction · 5 distinct chains · 93% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cgmp dependent protein kinase	protein	53	87% helix, 0% strand	Q6P5T7
B	Cgmp dependent protein kinase	protein	47	96% helix, 0% strand	Q6P5T7
C	Cgmp dependent protein kinase	protein	53	92% helix, 0% strand	Q6P5T7
D	Cgmp dependent protein kinase	protein	50	92% helix, 0% strand	Q6P5T7
E	Cgmp dependent protein kinase	protein	51	96% helix, 0% strand	Q6P5T7

Ligands and binding sites

HEZ · Hexane-1,6-diol · additive · 7 copies · chains A, C, D, E
GOL · Glycerol · additive · chains D, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	137	0.52	0.80	18	empty
2	93	0.39	0.76	16	empty
3	53	0.30	0.76	13	empty
4	54	0.25	0.73	13	HEZ, GOL

Interfaces

7 interfaces between chains.

C–D · 1391 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1382 Å² buried · 10 hydrogen bonds · protein-protein
D–E · 725 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 334 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 265 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 modified (engineered).

Compared structures

3NMD · Crystal structure of the leucine zipper domain of cGMP dependent protein kinase I beta · the same entry in another collection · chain A against A, 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 Q6P5T7
Elsewhere: RCSB PDB 3NMD · PDBe 3NMD · UniProt Q6P5T7

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