MolNFT v1 · #176800 · protein

Crystal structure of the chemically synthesized MK2H_DELTAMILPYS peptide homodimer in complex with malonate

7DXZ · MK2H_DELTAMILPYS protein: “Crystal structure of the chemically synthesized MK2H_DELTAMILPYS peptide homodimer in complex with malonate”. X-ray diffraction, 2 pockets (best druggability 0.53). MolNFT v1 #176800 on GenesisL1: 3D…

PDB: 7DXZ
Type: protein
Length: 169 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MK2H_DELTAMILPYS protein
Pockets: 2 · best druggability 0.53

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	MK2H_DELTAMILPYS protein	protein	42	24% helix, 0% strand	—
D	MK2H_DELTAMILPYS protein	protein	43	23% helix, 0% strand	—

Ligands and binding sites

MLA · Malonic acid · additive · 7 copies · chains A, D, B, C

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	209	0.53	0.77	24	empty
2	267	0.51	0.74	35	empty

Interfaces

5 interfaces between chains.

B–C · 2174 Å² buried · 46 hydrogen bonds · protein-protein
C–D · 191 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 155 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 64 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 59 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7DXZ · Crystal structure of the chemically synthesized mk2h_deltaMILPYS peptide homodimer in… · 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
Elsewhere: RCSB PDB 7DXZ · PDBe 7DXZ

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