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Structure of the human MESH1-NADPH complex

Analyse Structure of the human MESH1-NADPH complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VXA
Type: protein
Length: 356 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanosine-3',5'-BIS(DIPHOSPHATE) 3'-pyrophosphohydrolase MESH1
EC: 3.1.7.2
UniProt: Q8N4P3
Ligands: NDP, ZN, NA
Pockets: 4 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 66% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Guanosine-3',5'-BIS(DIPHOSPHATE) 3'-pyrophosphohydrolase MESH1 (EC 3.1.7.2)	protein	178	66% helix, 1% strand	Q8N4P3

Ligands and binding sites

NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B
NA · Sodium ion · metal
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B

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

Pockets

4 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	419	0.71	0.82	44	NDP
2	389	0.70	0.82	40	NDP, NA
3	147	0.48	0.78	18	empty
4	156	0.46	0.76	17	empty

Interfaces

1 interface between chains.

A–B · 1292 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (additive adduct).

Compared structures

5VXA · Structure of the human Mesh1-NADPH complex · the same entry in another collection · chain A against A, TM-score 1.00
Q8N4P3 · AlphaFold monomer V2.0 prediction for guanosine-3',5'-BIS(DIPHOSPHATE)… · a predicted model of the same protein · 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 Q8N4P3
Elsewhere: RCSB PDB 5VXA · PDBe 5VXA · UniProt Q8N4P3

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