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Crystal structure of ME1 in complex with NADPH

Analyse Crystal structure of ME1 in complex with NADPH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7X12
Type: protein
Length: 2,256 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NADP-dependent malic enzyme
EC: 1.1.1.40
UniProt: P48163
Ligands: NDP, MN
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	NADP-dependent malic enzyme (EC 1.1.1.40)	protein	564	48% helix, 10% strand	P48163

Ligands and binding sites

NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	535	0.84	0.90	92	empty
2	149	0.78	0.95	32	empty
3	156	0.78	0.94	38	empty
4	86	0.76	0.98	17	empty
5	560	0.76	0.83	49	NDP

Interfaces

6 interfaces between chains.

A–B · 2317 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 2311 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 1362 Å² buried · 19 hydrogen bonds · protein-protein
A–D · 1356 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 1191 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

7X12 · Crystal structure of ME1 in complex with NADPH · the same entry in another collection · chain A against A, TM-score 1.00
P48163 · AlphaFold monomer V2.0 prediction for NADP-dependent malic enzyme (P48163) · a predicted model of the same protein · chain A 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 P48163
Elsewhere: RCSB PDB 7X12 · PDBe 7X12 · UniProt P48163

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