6YNH: Glyceraldehyde-3-phosphate dehydrogenase

GAPDH purified from the supernatant of HEK293F cells: crystal form 4 of 4. Determined by X-ray diffraction at 2.62 Å resolution. Released 6 May 2020.

Method: X-ray diffraction
Resolution: 2.62 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,327
Mol. weight: 146.55 kDa
Ligands: XPE
Released: 6 May 2020

Explore 6YNH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YNH contains 60 α-helices and 77 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.

Chain B: 15 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	3-4	2
β-strand	5-9	5	1
α-helix	13-25	13
β-strand	29-34	6	1
α-helix	40-48	9
β-strand	60-63	4	2
β-strand	66-69	4	2
β-strand	72-74	3	2
β-strand	75-77	3	1
α-helix	82-84	3
α-helix	87-90	4
β-strand	94-97	4	1
α-helix	105-108	4
α-helix	110-113	4
β-strand	118-121	4	1
β-strand	130	1	1
α-helix	137-139	3
β-strand	146-148	3	1
α-helix	152-167	16
β-strand	170-179	10	3
β-strand	186	1	4
α-helix	196-199	4
β-strand	201	1	4
β-strand	207-210	4	3
α-helix	213-220	8
α-helix	222-224	3
β-strand	228-234	7	3
β-strand	241-249	9	3
α-helix	255-267	13
β-strand	274-277	4	3
α-helix	283-286	4
β-strand	293-296	4	3
β-strand	301-304	4	3
β-strand	307-314	8	3
α-helix	318-334	17

Chain D: 15 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	5
α-helix	13-25	13
β-strand	29-34	6	5
α-helix	40-48	9
β-strand	60-63	4	5
β-strand	66-69	4	5
β-strand	72-77	6	5
α-helix	82-84	3
α-helix	87-90	4
β-strand	94-97	4	5
α-helix	105-108	4
α-helix	110-113	4
β-strand	118-121	4	5
α-helix	129	1
β-strand	130	1	5
α-helix	137-139	3
β-strand	146-148	3	5
α-helix	152-167	16
β-strand	170-179	10	6
β-strand	186	1	7
α-helix	196-199	4
β-strand	201	1	7
β-strand	207-210	4	6
α-helix	213-220	8
α-helix	222-224	3
β-strand	228-234	7	6
β-strand	241-249	9	6
α-helix	255-267	13
β-strand	274-277	4	6
α-helix	283-286	4
β-strand	293-296	4	6
β-strand	301-304	4	6
β-strand	307-314	8	6
α-helix	318-334	17

Chain F: 15 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	3-4	2
β-strand	5-9	5	8
α-helix	13-25	13
β-strand	29-34	6	8
α-helix	40-48	9
β-strand	60-63	4	8
β-strand	66-69	4	8
β-strand	72-77	6	8
α-helix	82-84	3
α-helix	87-90	4
β-strand	94-97	4	8
α-helix	105-108	4
α-helix	109-112	4
β-strand	118-121	4	8
β-strand	130	1	8
α-helix	137-139	3
β-strand	146-148	3	8
α-helix	152-167	16
β-strand	170-179	10	9
β-strand	186	1	10
α-helix	196-199	4
β-strand	201	1	10
β-strand	207-210	4	9
α-helix	213-220	8
α-helix	222-224	3
β-strand	228-234	7	9
β-strand	241-249	9	9
α-helix	255-267	13
β-strand	274-277	4	9
α-helix	283-286	4
β-strand	293-296	4	9
β-strand	301-304	4	9
β-strand	307-314	8	9
α-helix	318-334	17

Chain G: 15 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	3-4	2
β-strand	5-9	5	11
α-helix	13-25	13
β-strand	29-34	6	11
α-helix	40-48	9
β-strand	60-63	4	11
β-strand	66-69	4	11
β-strand	72-77	6	11
α-helix	82-84	3
α-helix	87-90	4
β-strand	94-97	4	11
α-helix	105-108	4
α-helix	110-113	4
β-strand	118-121	4	11
β-strand	130	1	11
α-helix	137-139	3
β-strand	146-148	3	11
α-helix	152-167	16
β-strand	170-179	10	12
β-strand	186	1	13
α-helix	196-199	4
β-strand	201	1	13
β-strand	207-210	4	12
α-helix	213-220	8
α-helix	222-224	3
β-strand	228-234	7	12
β-strand	241-249	9	12
α-helix	255-267	13
β-strand	274-277	4	12
α-helix	283-286	4
β-strand	293-296	4	12
β-strand	301-304	4	12
β-strand	307-314	8	12
α-helix	318-334	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glyceraldehyde-3-phosphate dehydrogenase	B, D, F, G	protein	335	Homo sapiens	P04406 (AlphaFold model)

Sequence of entity 1 (B, D, F, G), FASTA

>6YNH_1 Glyceraldehyde-3-phosphate dehydrogenase (chains B, D, F, G)
MGKVKVGVNGFGRIGRLVTRAAFNSGKVDIVAINDPFIDLNYMVYMFQYDSTHGKFHGTV
KAENGKLVINGNPITIFQERDPSKIKWGDAGAEYVVESTGVFTTMEKAGAHLQGGAKRVI
ISAPSADAPMFVMGVNHEKYDNSLKIISNASCTTNCLAPLAKVIHDNFGIVEGLMTTVHA
ITATQKTVDGPSGKLWRDGRGALQNIIPASTGAAKAVGKVIPELNGKLTGMAFRVPTANV
SVVDLTCRLEKPAKYDDIKKVVKQASEGPLKGILGYTEHQVVSSDFNSDTHSSTFDAGAG
IALNDHFVKLISWYDNEFGYSNRVVDLMAHMASKE

Ligands and cofactors

ID	Name	Formula	Copies
XPE	3,6,9,12,15,18,21,24,27-nonaoxanonacosane-1,29-diol	C20 H42 O11	4

Primary citation

Partial catalytic Cys oxidation of human GAPDH to Cys-sulfonic acid. Lia, A., Dowle, A., Taylor, C. et al. Wellcome Open Res (2020) 5:114-114. DOI 10.12688/wellcomeopenres.15893.2 · PubMed

Other PDB entries of the same protein (UniProt P04406 (AlphaFold model), which also has an AlphaFold model), best resolution first:

27FM 1.46 Å, Crystal structure of human glyceraldehyde-3-phosphate dehydrogenase bound to gold(I)
6YND 1.52 Å, GAPDH purified from the supernatant of HEK293F cells: crystal form 1 of 4.
1U8F 1.75 Å, Crystal Structure Of Human Placental Glyceraldehyde-3-Phosphate Dehydrogenase At 1.75…
9L3E 1.77 Å, Structure of GAPDH complexed with Leu-F
8P5F 1.82 Å, Human wild-type GAPDH,orthorhombic form
6M61 1.82 Å, Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) with inhibitor heptelidic acid
6YNE 1.85 Å, GAPDH purified from the supernatant of HEK293F cells: crystal form 2 of 4.
9UNY 1.87 Å, Natural product inhibitor of glyceraldehyde-3-phosphate dehydrogenase(GAPDH)
8G17 1.98 Å, CryoEM structure of wild-type GAPDH
4WNC 1.99 Å, Crystal structure of human wild-type GAPDH at 1.99 angstroms resolution
8G15 2.07 Å, CryoEM structure of nuclear GAPDH under 24h Oxidative Stress
8G16 2.07 Å, CryoEM structure of cytoplasmic GAPDH under 24h Oxidative Stress

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