6IQ6: GAPDH

Crystal structure of GAPDH. Determined by X-ray diffraction at 2.29 Å resolution. Released 28 Aug 2019.

Method: X-ray diffraction
Resolution: 2.29 Å
Organism: Homo sapiens
Chains: 8
Atoms: 20,298
Mol. weight: 289.44 kDa
Ligands: AW9
Released: 28 Aug 2019

Explore 6IQ6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6IQ6 contains 114 α-helices and 147 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: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
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
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	152-168	17
β-strand	170-180	11	3
α-helix	196-199	4
β-strand	207-210	4	3
α-helix	213-220	8
α-helix	222-224	3
β-strand	228-235	8	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	318-332	15

Chain B: 15 helices, 19 β-strands

Element	Residues	Length	Sheet
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
α-helix	87-90	4
β-strand	94-97	4	4
α-helix	105-108	4
α-helix	109-112	4
β-strand	118-121	4	4
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
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	293-296	4	5
α-helix	297-299	3
β-strand	301-304	4	5
β-strand	307-314	8	5
α-helix	318-333	16

Chain C: 14 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	7
α-helix	13-25	13
β-strand	29-34	6	7
α-helix	40-48	9
β-strand	60-63	4	7
β-strand	66-69	4	7
β-strand	72-77	6	7
α-helix	82-84	3
α-helix	87-90	4
β-strand	94-97	4	7
α-helix	105-108	4
α-helix	110-113	4
β-strand	118-121	4	7
β-strand	130	1	7
α-helix	137-139	3
β-strand	146-148	3	7
α-helix	152-167	16
β-strand	170-179	10	8
β-strand	186	1	9
α-helix	196-199	4
β-strand	201	1	9
β-strand	207-210	4	8
α-helix	213-220	8
α-helix	222-224	3
β-strand	228-234	7	8
β-strand	241-249	9	8
α-helix	255-267	13
β-strand	274-277	4	8
α-helix	283-286	4
β-strand	293-296	4	8
β-strand	301-304	4	8
β-strand	307-314	8	8
α-helix	318-332	15

Chain D: 14 helices, 17 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
α-helix	87-90	4
β-strand	94-97	4	10
α-helix	105-108	4
α-helix	110-113	4
β-strand	118-121	4	10
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	196-199	4
β-strand	207-210	4	11
α-helix	213-220	8
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	293-296	4	11
β-strand	301-304	4	11
β-strand	307-314	8	11
α-helix	318-332	15

Chain E: 14 helices, 19 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	13
β-strand	66-69	4	13
β-strand	72-74	3	13
β-strand	75-77	3	12
α-helix	82-84	3
α-helix	87-90	4
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	152-167	16
β-strand	170-179	10	14
β-strand	186	1	15
α-helix	196-199	4
β-strand	201	1	15
β-strand	207-210	4	14
α-helix	213-220	8
α-helix	222-224	3
β-strand	228-234	7	14
β-strand	241-249	9	14
α-helix	255-267	13
β-strand	274-277	4	14
α-helix	283-286	4
β-strand	293-302	10	14
β-strand	307-314	8	14
α-helix	318-332	15

Chain F: 15 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	16
α-helix	13-25	13
β-strand	29-34	6	16
α-helix	40-48	9
β-strand	60-63	4	16
β-strand	66-69	4	16
β-strand	72-77	6	16
α-helix	82-84	3
α-helix	87-90	4
β-strand	94-97	4	16
α-helix	105-108	4
α-helix	110-113	4
β-strand	118-121	4	16
β-strand	130	1	16
α-helix	137-139	3
β-strand	146-148	3	16
α-helix	152-168	17
β-strand	170-179	10	17
α-helix	196-199	4
β-strand	207-210	4	17
α-helix	213-220	8
α-helix	222-224	3
β-strand	228-234	7	17
β-strand	241-249	9	17
α-helix	255-267	13
β-strand	274-277	4	17
α-helix	283-286	4
β-strand	293-296	4	17
α-helix	297-299	3
β-strand	301-304	4	17
β-strand	307-314	8	17
α-helix	318-334	17

Chain G: 16 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	19
β-strand	66-69	4	19
β-strand	72-74	3	19
β-strand	75-77	3	18
α-helix	82-84	3
α-helix	87-90	4
β-strand	94-97	4	18
α-helix	105-108	4
α-helix	109-112	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	152-168	17
β-strand	170-179	10	20
α-helix	196-199	4
β-strand	207-210	4	20
α-helix	217-220	4
α-helix	222-224	3
β-strand	228-234	7	20
β-strand	241-249	9	20
α-helix	255-267	13
β-strand	274-277	4	20
α-helix	283-286	4
β-strand	293-296	4	20
α-helix	297-299	3
β-strand	301-304	4	20
β-strand	307-314	8	20
α-helix	318-333	16

Chain H: 13 helices, 20 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	22
β-strand	66-69	4	22
β-strand	72-74	3	22
β-strand	75-77	3	21
α-helix	82-84	3
α-helix	87-90	4
β-strand	94-97	4	21
α-helix	105-113	9
β-strand	118-121	4	21
α-helix	129	1
β-strand	130	1	21
β-strand	146-148	3	21
α-helix	154-167	14
β-strand	170-180	11	23
β-strand	186	1	24
α-helix	196-199	4
β-strand	201	1	24
β-strand	207-210	4	23
α-helix	217-220	4
α-helix	222-224	3
β-strand	228-235	8	23
β-strand	241-249	9	23
α-helix	255-267	13
β-strand	274-277	4	23
α-helix	283-286	4
β-strand	293-296	4	23
β-strand	301-304	4	23
β-strand	307-314	8	23
α-helix	318-332	15

Molecules and chains

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

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

>6IQ6_1 Glyceraldehyde-3-phosphate dehydrogenase (chains A, B, C, D, E, F, G, H)
MGKVKVGVNGFGRIGRLVTRAAFNSGKVDIVAINDPFIDLNYMVYMFQYDSTHGKFHGTV
KAENGKLVINGNPITIFQERDPSKIKWGDAGAEYVVESTGVFTTMEKAGAHLQGGAKRVI
ISAPSADAPMFVMGVNHEKYDNSLKIISNASCTTNCLAPLAKVIHDNFGIVEGLMTTVHA
ITATQKTVDGPSGKLWRDGRGALQNIIPASTGAAKAVGKVIPELNGKLTGMAFRVPTANV
SVVDLTCRLEKPAKYDDIKKVVKQASEGPLKGILGYTEHQVVSSDFNSDTHSSTFDAGAG
IALNDHFVKLISWYDNEFGYSNRVVDLMAHMASKE

Ligands and cofactors

ID	Name	Formula	Copies
AW9	(2Z)-4-methoxy-4-oxobut-2-enoic acid	C5 H6 O4	5

Primary citation

Structural Study of Monomethyl Fumarate-Bound Human GAPDH. Park, J.B., Park, H., Son, J. et al. Mol Cells (2019) 42:597-603. DOI 10.14348/molcells.2019.0114 · 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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