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Crystal structure of human ME2 R484W

Analyse Crystal structure of human ME2 R484W in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7BSJ
Type: protein
Length: 1,105 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NAD-dependent malic enzyme, mitochondrial
EC: 1.1.1.38
UniProt: P23368
Ligands: NAD, FUM, TTN, MG
Pockets: 15 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NAD-dependent malic enzyme, mitochondrial (EC 1.1.1.38)	protein	553	46% helix, 10% strand	P23368
B	NAD-dependent malic enzyme, mitochondrial (EC 1.1.1.38)	protein	552	48% helix, 9% strand	P23368

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B
FUM · Fumaric acid · ligand · 2 copies · chains A, B
TTN · Tartronate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	191	0.83	0.97	35	empty
2	821	0.81	0.83	88	empty
3	330	0.72	0.84	38	FUM
4	53	0.71	0.98	17	FUM
5	384	0.68	0.81	48	NAD, MG, TTN

Interfaces

1 interface between chains.

A–B · 2351 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

7BSJ · Crystal structure of human ME2 R484W · the same entry in another collection · chain A against A, TM-score 1.00
P23368 · AlphaFold monomer V2.0 prediction for NAD-dependent malic enzyme, mitochondrial (P23368) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P23368
Elsewhere: RCSB PDB 7BSJ · PDBe 7BSJ · UniProt P23368

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