MolNFT v1 · #93480 · protein

Crystal structure of human ERK2 complexed with a MAPK docking peptide

4H3P · Mitogen-activated protein kinase 1: “Crystal structure of human ERK2 complexed with a MAPK docking peptide”. X-ray diffraction, 1 ligand (ANP), 8 pockets (best druggability 0.74). MolNFT v1 #93480 on GenesisL1: 3D structure, binding…

PDB: 4H3P
Type: protein
Length: 713 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mitogen-activated protein kinase 1; Ribosomal protein S6 kinase alpha-1
EC: 2.7.11.24, 2.7.11.1
UniProt: P28482, Q15418
Ligands: ANP
Pockets: 8 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 36% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mitogen-activated protein kinase 1 (EC 2.7.11.24)	protein	342	35% helix, 15% strand	P28482
D	Mitogen-activated protein kinase 1 (EC 2.7.11.24)	protein	338	36% helix, 16% strand	P28482
B	Ribosomal protein S6 kinase alpha-1 (EC 2.7.11.1)	protein	16	44% helix, 0% strand	Q15418
E	Ribosomal protein S6 kinase alpha-1 (EC 2.7.11.1)	protein	17	41% helix, 0% strand	Q15418

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	863	0.74	0.78	74	ANP
2	461	0.72	0.82	42	ANP
3	103	0.55	0.84	23	empty
4	327	0.55	0.75	41	empty
5	147	0.49	0.78	22	empty

Interfaces

3 interfaces between chains.

D–E · 763 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 745 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 534 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4H3P · Crystal structure of human ERK2 complexed with a MAPK docking peptide · the same entry in another collection · chain A against A, TM-score 1.00
Q15418 · AlphaFold monomer V2.0 prediction for ribosomal protein S6 kinase alpha-1 (Q15418) · a predicted model of the same protein · chain B against A, TM-score 0.49

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 P28482
Every structure of UniProt Q15418
Elsewhere: RCSB PDB 4H3P · PDBe 4H3P · UniProt P28482 · UniProt Q15418

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