6YNF: Glyceraldehyde-3-phosphate dehydrogenase

GAPDH purified from the supernatant of HEK293F cells: crystal form 3 of 4. Determined by X-ray diffraction at 2.39 Å resolution. Released 6 May 2020.

Method: X-ray diffraction
Resolution: 2.39 Å
Organism: Homo sapiens
Chains: 8
Atoms: 21,150
Mol. weight: 291.59 kDa
Ligands: XPE
Released: 6 May 2020

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

Secondary structure: helices and β-sheets

6YNF contains 123 α-helices and 142 β-strands across 8 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 A: 16 helices, 18 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	1
β-strand	66-69	4	1
β-strand	72-77	6	1
α-helix	82-84	3
β-strand	94-97	4	1
α-helix	105-108	4
α-helix	110-113	4
β-strand	118-121	4	1
α-helix	129	1
β-strand	130	1	1
α-helix	137-139	3
β-strand	146-148	3	1
α-helix	152-168	17
β-strand	170-179	10	2
α-helix	180-181	2
β-strand	186	1	3
α-helix	196-199	4
β-strand	201	1	3
β-strand	207-210	4	2
α-helix	213-217	5
α-helix	222-224	3
β-strand	228-234	7	2
β-strand	241-249	9	2
α-helix	255-267	13
β-strand	274-277	4	2
α-helix	283-286	4
β-strand	293-304	12	2
β-strand	307-314	8	2
α-helix	318-334	17

Chains B and C: 16 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	3-4	2
β-strand	5-9	5	4
α-helix	13-25	13
β-strand	29-34	6	4
α-helix	40-48	9
β-strand	60-63	4	4
β-strand	66-69	4	4
β-strand	72-77	6	4
α-helix	82-84	3
β-strand	94-97	4	4
α-helix	105-108	4
α-helix	110-113	4
β-strand	118-121	4	4
α-helix	129	1
β-strand	130	1	4
α-helix	137-139	3
β-strand	146-148	3	4
α-helix	152-168	17
β-strand	170-179	10	5
α-helix	180-181	2
β-strand	186	1	6
α-helix	196-199	4
β-strand	201	1	6
β-strand	207-210	4	5
α-helix	213-220	8
α-helix	222-224	3
β-strand	228-234	7	5
β-strand	241-249	9	5
α-helix	255-267	13
β-strand	274-277	4	5
α-helix	283-286	4
β-strand	293-304	12	5
β-strand	307-314	8	5
α-helix	318-334	17

Chain D: 15 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	10
α-helix	13-25	13
β-strand	29-34	6	10
α-helix	40-48	9
β-strand	60-63	4	10
β-strand	66-69	4	10
β-strand	72-77	6	10
α-helix	82-84	3
β-strand	94-97	4	10
α-helix	105-108	4
α-helix	110-113	4
β-strand	118-121	4	10
α-helix	129	1
β-strand	130	1	10
α-helix	137-139	3
β-strand	146-148	3	10
α-helix	152-168	17
β-strand	170-179	10	11
α-helix	180-181	2
α-helix	196-199	4
β-strand	207-210	4	11
α-helix	217-220	4
α-helix	222-224	3
β-strand	228-234	7	11
β-strand	241-249	9	11
α-helix	255-267	13
β-strand	274-277	4	11
α-helix	283-286	4
β-strand	293-304	12	11
β-strand	307-314	8	11
α-helix	318-334	17

Chain E: 14 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	12
α-helix	13-25	13
β-strand	29-34	6	12
α-helix	40-48	9
β-strand	60-63	4	12
β-strand	66-69	4	12
β-strand	72-77	6	12
α-helix	82-84	3
β-strand	94-97	4	12
α-helix	105-108	4
α-helix	110-113	4
β-strand	118-121	4	12
β-strand	130	1	12
α-helix	137-139	3
β-strand	146-148	3	12
α-helix	152-168	17
β-strand	170-179	10	13
α-helix	180-181	2
β-strand	186	1	14
α-helix	196-199	4
β-strand	201	1	14
β-strand	207-210	4	13
α-helix	213-220	8
α-helix	222-224	3
β-strand	228-234	7	13
β-strand	241-249	9	13
α-helix	255-267	13
β-strand	274-277	4	13
α-helix	283-286	4
β-strand	293-302	10	13
β-strand	307-314	8	13
α-helix	318-334	17

Chain F: 16 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	3-4	2
β-strand	5-9	5	15
α-helix	13-25	13
β-strand	29-34	6	15
α-helix	40-48	9
β-strand	60-63	4	15
β-strand	66-69	4	15
β-strand	72-77	6	15
α-helix	82-84	3
β-strand	94-97	4	15
α-helix	105-108	4
α-helix	110-114	5
β-strand	118-121	4	15
α-helix	129	1
β-strand	130	1	15
α-helix	137-139	3
β-strand	146-148	3	15
α-helix	152-168	17
β-strand	170-179	10	16
α-helix	180-181	2
β-strand	186	1	17
α-helix	196-199	4
β-strand	201	1	17
β-strand	207-210	4	16
α-helix	213-220	8
α-helix	222-224	3
β-strand	228-234	7	16
β-strand	241-249	9	16
α-helix	255-267	13
β-strand	274-277	4	16
α-helix	283-286	4
β-strand	293-304	12	16
β-strand	307-314	8	16
α-helix	318-334	17

Chain G: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	18
α-helix	13-25	13
β-strand	29-34	6	18
α-helix	40-48	9
β-strand	60-63	4	18
β-strand	66-69	4	18
β-strand	72-77	6	18
α-helix	82-84	3
β-strand	94-97	4	18
α-helix	105-108	4
α-helix	110-113	4
β-strand	118-121	4	18
α-helix	129	1
β-strand	130	1	18
α-helix	137-139	3
β-strand	146-148	3	18
α-helix	154-168	15
β-strand	170-179	10	19
α-helix	180-181	2
β-strand	186	1	20
α-helix	196-199	4
β-strand	201	1	20
β-strand	207-210	4	19
α-helix	217-220	4
α-helix	222-224	3
β-strand	228-234	7	19
β-strand	241-249	9	19
α-helix	255-267	13
β-strand	274-277	4	19
α-helix	283-286	4
β-strand	293-304	12	19
β-strand	307-314	8	19
α-helix	318-334	17

Chain H: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	21
α-helix	13-25	13
β-strand	29-34	6	21
α-helix	40-48	9
β-strand	60-63	4	21
β-strand	66-69	4	21
β-strand	72-77	6	21
α-helix	82-84	3
β-strand	94-97	4	21
α-helix	105-108	4
α-helix	109-114	6
β-strand	118-121	4	21
α-helix	129	1
β-strand	130	1	21
α-helix	137-139	3
β-strand	146-148	3	21
α-helix	152-168	17
β-strand	170-179	10	22
α-helix	180-181	2
β-strand	186	1	23
α-helix	196-199	4
β-strand	201	1	23
β-strand	207-210	4	22
α-helix	213-217	5
α-helix	222-224	3
β-strand	228-234	7	22
β-strand	241-249	9	22
α-helix	255-267	13
β-strand	274-277	4	22
α-helix	283-286	4
β-strand	293-304	12	22
β-strand	307-314	8	22
α-helix	318-334	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glyceraldehyde-3-phosphate dehydrogenase	A, B, C, D, E, F, G, H	protein	334	Homo sapiens	P04406 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>6YNF_1 Glyceraldehyde-3-phosphate dehydrogenase (chains A, B, C, D, E, F, G, H)
GKVKVGVNGFGRIGRLVTRAAFNSGKVDIVAINDPFIDLNYMVYMFQYDSTHGKFHGTVK
AENGKLVINGNPITIFQERDPSKIKWGDAGAEYVVESTGVFTTMEKAGAHLQGGAKRVII
SAPSADAPMFVMGVNHEKYDNSLKIISNASCTTNCLAPLAKVIHDNFGIVEGLMTTVHAI
TATQKTVDGPSGKLWRDGRGALQNIIPASTGAAKAVGKVIPELNGKLTGMAFRVPTANVS
VVDLTCRLEKPAKYDDIKKVVKQASEGPLKGILGYTEHQVVSSDFNSDTHSSTFDAGAGI
ALNDHFVKLISWYDNEFGYSNRVVDLMAHMASKE

Ligands and cofactors

ID	Name	Formula	Copies
XPE	3,6,9,12,15,18,21,24,27-nonaoxanonacosane-1,29-diol	C20 H42 O11	7

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

Browse structure collections

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