7SNI: G6PD-D200N tetramer

Structure of G6PD-D200N tetramer bound to NADP+ and G6P. Determined by electron microscopy at 2.5 Å resolution. Released 13 Jul 2022.

Method: Electron microscopy
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 16,533
Mol. weight: 248.6 kDa
Ligands: NAP, BG6
Released: 13 Jul 2022

Explore 7SNI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SNI contains 126 α-helices and 72 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A and B: 31 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	29-31	3
β-strand	32-37	6	1
α-helix	42-43	2
α-helix	44-48	5
α-helix	49-57	9
β-strand	65-71	7	1
α-helix	77-88	12
α-helix	92-94	3
α-helix	95-103	9
β-strand	105-109	5	1
α-helix	115-127	13
α-helix	134	1
β-strand	135-140	6	1
α-helix	144-146	3
α-helix	147-157	11
β-strand	165-169	5	1
α-helix	177-188	12
β-strand	196-198	3	1
α-helix	201-204	4
α-helix	206-216	11
β-strand	230-238	9	2
α-helix	247-255	9
α-helix	256-264	9
α-helix	265-272	8
α-helix	273-276	4
α-helix	281-292	12
β-strand	295	1	3
α-helix	296-299	4
α-helix	300-302	3
β-strand	303-309	7	2
α-helix	316-319	4
α-helix	322-324	3
α-helix	329	1
β-strand	337-343	7	2
β-strand	344	1	3
β-strand	353-359	7	2
β-strand	366-373	8	2
α-helix	374-376	3
β-strand	389-395	7	2
β-strand	399-407	9	2
α-helix	408	1
β-strand	415-423	9	2
α-helix	433-435	3
α-helix	436-446	11
β-strand	453	1	1
α-helix	455-475	21
α-helix	477-479	3
β-strand	480-483	4	2
α-helix	490-499	10

Chains C and D: 32 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	29-31	3
β-strand	32-37	6	6
α-helix	42-43	2
α-helix	44-48	5
α-helix	49-57	9
β-strand	65-71	7	6
α-helix	77-88	12
α-helix	92-94	3
α-helix	95-103	9
β-strand	105-109	5	6
α-helix	115-127	13
α-helix	134	1
β-strand	135-140	6	6
α-helix	144-146	3
α-helix	147-157	11
β-strand	165-169	5	6
α-helix	177-190	14
β-strand	196-198	3	6
α-helix	201-204	4
α-helix	206-216	11
β-strand	230-238	9	7
α-helix	247-251	5
α-helix	254-255	2
α-helix	256-264	9
α-helix	265-272	8
α-helix	273-276	4
α-helix	281-292	12
β-strand	295	1	8
α-helix	296-299	4
α-helix	300-302	3
β-strand	303-309	7	7
α-helix	316-319	4
α-helix	322-324	3
α-helix	329	1
β-strand	337-343	7	7
β-strand	344	1	8
β-strand	353-359	7	7
β-strand	366-373	8	7
α-helix	374-376	3
β-strand	389-395	7	7
β-strand	399-407	9	7
α-helix	408	1
β-strand	415-423	9	7
α-helix	433-435	3
α-helix	436-446	11
β-strand	453	1	6
α-helix	455-475	21
α-helix	477-479	3
β-strand	480-483	4	7
α-helix	490-499	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glucose-6-phosphate 1-dehydrogenase	A, B, C, D	protein	523	Homo sapiens	P11413 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>7SNI_1 Glucose-6-phosphate 1-dehydrogenase (chains A, B, C, D)
MAEQVALSRTQVCGILREELFQGDAFHQSDTHIFIIMGASGDLAKKKIYPTIWWLFRDGL
LPENTFIVGYARSRLTVADIRKQSEPFFKATPEEKLKLEDFFARNSYVAGQYDDAASYQR
LNSHMNALHLGSQANRLFYLALPPTVYEAVTKNIHESCMSQIGWNRIIVEKPFGRDLQSS
DRLSNHISSLFREDQIYRINHYLGKEMVQNLMVLRFANRIFGPIWNRDNIACVILTFKEP
FGTEGRGGYFDEFGIIRDVMQNHLLQMLCLVAMEKPASTNSDDVRDEKVKVLKCISEVQA
NNVVLGQYVGNPDGEGEATKGYLDDPTVPRGSTTATFAAVVLYVENERWDGVPFILRCGK
ALNERKAEVRLQFHDVAGDIFHQQCKRNELVIRVQPNEAVYTKMMTKKPGMFFNPEESEL
DLTYGNRYKNVKLPDAYERLILDVFCGSQMHFVRSDELREAWRIFTPLLHQIELEKPKPI
PYIYGSRGPTEADELMKRVGFQYEGTYKWVNPHKLLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAP	NADP nicotinamide-adenine-dinucleotide phosphate	C21 H28 N7 O17 P3	8
BG6	6-O-phosphono-beta-D-glucopyranose	C6 H13 O9 P	4

Primary citation

Allosteric role of a structural NADP + molecule in glucose-6-phosphate dehydrogenase activity. Wei, X., Kixmoeller, K., Baltrusaitis, E. et al. Proc Natl Acad Sci U S A (2022) 119:e2119695119-e2119695119. DOI 10.1073/pnas.2119695119 · PubMed

Other PDB entries of the same protein (UniProt P11413 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6JYU 1.89 Å, Crystal structure of Human G6PD Canton
6E08 1.9 Å, Crystal structure of G6PD in complex with structural NADP
7SNH 2.2 Å, Structure of G6PD-D200N tetramer bound to NADP+
7ZVE 2.28 Å, K403 acetylated glucose-6-phosphate dehydrogenase (G6PD)
7ZVD 2.46 Å, K89 acetylated glucose-6-phosphate dehydrogenase (G6PD) in a complex with structural NADP+
2BH9 2.5 Å, X-ray structure of a deletion variant of human glucose 6-phosphate dehydrogenase…
7UC2 2.5 Å, Structure of G6PD-D200N tetramer bound to NADP+ with no symmetry applied
6E07 2.6 Å, Crystal structure of Canton G6PD in complex with structural NADP
5UKW 2.65 Å, Crystal structure of human Glucose 6-phosphate Dehydrogenase mutant (A277C) complexed…
7SNG 2.8 Å, structure of G6PD-WT tetramer
2BHL 2.9 Å, X-ray structure of human glucose-6-phosphate dehydrogenase (deletion variant) complexed…
7SEH 2.9 Å, Glucose-6-phosphate 1-dehydrogenase (K403QdLtL)

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