MolNFT v1 · #141284 · protein

Crystal structure of alpk-1 N-terminal domain in complex with ADP- heptose

5Z2C · Alpha-protein kinase 1: “Crystal structure of alpk-1 N-terminal domain in complex with ADP- heptose”. X-ray diffraction, 1 ligand (AYU), 20 pockets (best druggability 0.82). MolNFT v1 #141284 on GenesisL1: 3D structure, binding…

PDB: 5Z2C
Type: protein
Length: 3,876 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-protein kinase 1
EC: 2.7.11.-
UniProt: Q96QP1
Ligands: AYU
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 8 distinct chains · 71% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Alpha-protein kinase 1 (EC 2.7.11.-)	protein	445	70% helix, 0% strand	Q96QP1
C	Alpha-protein kinase 1 (EC 2.7.11.-)	protein	427	70% helix, 0% strand	Q96QP1
D	Alpha-protein kinase 1 (EC 2.7.11.-)	protein	434	71% helix, 0% strand	Q96QP1
E	Alpha-protein kinase 1 (EC 2.7.11.-)	protein	433	69% helix, 0% strand	Q96QP1
F	Alpha-protein kinase 1 (EC 2.7.11.-)	protein	433	71% helix, 0% strand	Q96QP1
G	Alpha-protein kinase 1 (EC 2.7.11.-)	protein	428	72% helix, 0% strand	Q96QP1
H	Alpha-protein kinase 1 (EC 2.7.11.-)	protein	423	72% helix, 0% strand	Q96QP1
I	Alpha-protein kinase 1 (EC 2.7.11.-)	protein	408	73% helix, 0% strand	Q96QP1

Ligands and binding sites

AYU · [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2S,3S,4S,5S,6R)-6-[(1S)-1,2-bis(oxidanyl)ethyl]-3,4, 5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate · ligand · 9 copies · chains A, B, C, D, E, F, G, H, I

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1000	0.82	0.83	80	empty
2	958	0.81	0.82	76	empty
3	853	0.81	0.83	72	empty
4	1068	0.80	0.82	80	empty
5	821	0.80	0.83	72	empty

Interfaces

15 interfaces between chains.

A–D · 1054 Å² buried · 14 hydrogen bonds · protein-protein
A–F · 1023 Å² buried · 14 hydrogen bonds · protein-protein
E–H · 930 Å² buried · 9 hydrogen bonds · protein-protein
B–F · 926 Å² buried · 10 hydrogen bonds · protein-protein
E–I · 903 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5Z2C · Crystal structure of ALPK-1 N-terminal domain in complex with ADP-heptose · the same entry in another collection · chain I against I, TM-score 1.00
Q96QP1 · AlphaFold monomer V2.0 prediction for alpha-protein kinase 1 (Q96QP1) · a predicted model of the same protein · chain B 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 Q96QP1
Elsewhere: RCSB PDB 5Z2C · PDBe 5Z2C · UniProt Q96QP1

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