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Structure of G6PD-D200N tetramer bound to NADP+

Analyse Structure of G6PD-D200N tetramer bound to NADP+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SNH
Type: protein
Length: 1,904 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucose-6-phosphate 1-dehydrogenase
EC: 1.1.1.49
UniProt: P11413
Ligands: NAP
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 1 distinct chain · 38% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49)	protein	476	38% helix, 22% strand	P11413

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 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, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1070	0.87	0.89	115	empty
2	67	0.66	0.93	22	empty
3	491	0.66	0.77	60	NAP
4	143	0.60	0.84	26	empty
5	267	0.59	0.78	29	NAP

Interfaces

6 interfaces between chains.

C–D · 2661 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 2657 Å² buried · 42 hydrogen bonds · protein-protein
A–C · 555 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 555 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 324 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7SNH · Structure of G6PD-D200N tetramer bound to NADP+ · the same entry in another collection · chain D against D, TM-score 1.00
P11413 · AlphaFold monomer V2.0 prediction for glucose-6-phosphate 1-dehydrogenase (P11413) · 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 P11413
Elsewhere: RCSB PDB 7SNH · PDBe 7SNH · UniProt P11413

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