MolNFT v1 · #111028 · protein

BETA2 carbohydrate binding module (cbm) of AMP-activated protein kinase (ampk) in complex with glucosyl-beta-cyclodextrin

4YEE · 5'-AMP-activated protein kinase subunit beta-2: “BETA2 carbohydrate binding module (cbm) of AMP-activated protein kinase (ampk) in complex with…”. X-ray diffraction, 1 ligand (GLC), 20 pockets (best druggability 0.76). MolNFT v1…

PDB: 4YEE
Type: protein
Length: 1,505 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-AMP-activated protein kinase subunit beta-2
UniProt: Q9QZH4
Ligands: GLC
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 5 distinct chains · 4% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, K, L	5'-AMP-activated protein kinase subunit beta-2	protein	82	4% helix, 57% strand	Q9QZH4
B, C, G	5'-AMP-activated protein kinase subunit beta-2	protein	83	4% helix, 52% strand	Q9QZH4
D	5'-AMP-activated protein kinase subunit beta-2	protein	79	4% helix, 54% strand	Q9QZH4
E, F, H, I, J, M, P	5'-AMP-activated protein kinase subunit beta-2	protein	85	4% helix, 55% strand	Q9QZH4
N, O, Q, R	5'-AMP-activated protein kinase subunit beta-2	protein	84	4% helix, 56% strand	Q9QZH4

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 144 copies · chains A, G, B, F, C, E, D, N, H, L, I, J, K, M, O, P, Q, R
GOL · Glycerol · additive · 19 copies · chains A, C, G, B, F, L, I, D, K, O, E, H, M, N, P

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	837	0.76	0.80	83	GOL
2	628	0.63	0.74	75	GOL
3	354	0.53	0.73	45	GLC
4	246	0.52	0.76	40	GOL
5	265	0.52	0.75	34	GLC, GOL

Interfaces

32 interfaces between chains.

E–I · 501 Å² buried · 6 hydrogen bonds · protein-protein
N–O · 487 Å² buried · 5 hydrogen bonds · protein-protein
G–M · 447 Å² buried · 5 hydrogen bonds · protein-protein
Q–R · 435 Å² buried · 1 hydrogen bond · protein-protein
B–L · 428 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4YEE · beta2 carbohydrate binding module (CBM) of AMP-activated protein kinase (AMPK) in complex… · the same entry in another collection · chain K against K, 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 Q9QZH4
Elsewhere: RCSB PDB 4YEE · PDBe 4YEE · UniProt Q9QZH4

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