MolNFT v1 · #63124 · protein

Crystal structure of human mkp-2

3EZZ · Dual specificity protein phosphatase 4: “Crystal structure of human mkp-2”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.76). MolNFT v1 #63124 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3EZZ
Type: protein
Length: 864 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dual specificity protein phosphatase 4
EC: 3.1.3.48, 3.1.3.16
UniProt: Q13115
Ligands: SO4
Pockets: 6 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Dual specificity protein phosphatase 4 (EC 3.1.3.48, 3.1.3.16)	protein	144	42% helix, 15% strand	Q13115

Ligands and binding sites

SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D, E, F

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

Pockets

6 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	772	0.76	0.81	72	empty
2	123	0.47	0.79	30	SO4
3	131	0.44	0.77	29	SO4
4	104	0.37	0.74	21	empty
5	56	0.36	0.79	16	empty

Interfaces

7 interfaces between chains.

E–F · 530 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 529 Å² buried · 6 hydrogen bonds · protein-protein
B–E · 468 Å² buried · 9 hydrogen bonds · protein-protein
A–E · 434 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 373 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3EZZ · Crystal Structure of human MKP-2 · the same entry in another collection · chain F against F, TM-score 1.00
Q13115 · AlphaFold monomer V2.0 prediction for dual specificity protein phosphatase 4 (Q13115) · a predicted model of the same protein · chain E against A, TM-score 0.98

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 Q13115
Elsewhere: RCSB PDB 3EZZ · PDBe 3EZZ · UniProt Q13115

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