Research workbench

Mddef in complex with mvapp, amppcp and magnesium

Analyse Mddef in complex with mvapp, amppcp and magnesium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6E2U
Type: protein
Length: 327 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mevalonate diphosphate decarboxylase
EC: 4.1.1.33
UniProt: Q9FD68
Ligands: DP6, ACP, MG
Pockets: 2 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mevalonate diphosphate decarboxylase (EC 4.1.1.33)	protein	327	41% helix, 26% strand	Q9FD68

Ligands and binding sites

DP6 · (3R)-3-hydroxy-5-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}-3-methylpentanoic acid · ligand · chains A
ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

2 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	522	0.70	0.80	56	DP6, ACP, MG
2	64	0.32	0.76	17	empty

Compared structures

6E2U · MDDEF in complex with MVAPP, AMPPCP and Magnesium · 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
Every structure of UniProt Q9FD68
Elsewhere: RCSB PDB 6E2U · PDBe 6E2U · UniProt Q9FD68

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