6M61: Glyceraldehyde-3-phosphate dehydrogenase

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) with inhibitor heptelidic acid. Determined by X-ray diffraction at 1.82 Å resolution. Released 30 Dec 2020.

Method: X-ray diffraction
Resolution: 1.82 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,441
Mol. weight: 148.08 kDa
Ligands: ZN, F4F, NAD
Released: 30 Dec 2020

Explore 6M61 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6M61 contains 56 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 O: 14 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
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	152-168	17
β-strand	170-179	10	3
α-helix	196-199	4
β-strand	207-210	4	3
α-helix	213-220	8
α-helix	222-224	3
β-strand	228-234	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	318-333	16

Chain P: 15 helices, 20 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	9
β-strand	66-69	4	9
β-strand	72-74	3	9
β-strand	75-77	3	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	152-168	17
β-strand	170-179	10	10
β-strand	186	1	11
α-helix	196-199	4
β-strand	201	1	11
β-strand	207-210	4	10
α-helix	213-220	8
α-helix	222-224	3
β-strand	228-234	7	10
β-strand	241-249	9	10
α-helix	255-267	13
β-strand	274-277	4	10
α-helix	283-286	4
β-strand	293-296	4	10
β-strand	301-304	4	10
β-strand	307-314	8	10
α-helix	318-333	16

Chain Q: 15 helices, 20 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	5
β-strand	66-69	4	5
β-strand	72-74	3	5
β-strand	75-77	3	4
α-helix	82-84	3
α-helix	87-90	4
β-strand	94-97	4	4
α-helix	105-108	4
α-helix	110-113	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	170-180	11	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	228-235	8	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	318-333	16

Chain R: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	12
α-helix	13-25	13
β-strand	30-33	4	12
α-helix	40-48	9
β-strand	60-62	3	13
β-strand	67-69	3	13
β-strand	76	1	12
α-helix	82-84	3
β-strand	94-96	3	12
β-strand	118-121	4	12
α-helix	129	1
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	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	293-296	4	14
β-strand	301-304	4	14
β-strand	307-314	8	14
α-helix	318-329	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glyceraldehyde-3-phosphate dehydrogenase	O, P, Q, R	protein	336	Homo sapiens	P04406 (AlphaFold model)

Sequence of entity 1 (O, P, Q, R), FASTA

>6M61_1 Glyceraldehyde-3-phosphate dehydrogenase (chains O, P, Q, R)
FMGKVKVGVNGFGRIGRLVTRAAFNSGKVDIVAINDPFIDLNYMVYMFQYDSTHGKFHGT
VKAENGKLVINGNPITIFQERDPSKIKWGDAGAEYVVESTGVFTTMEKAGAHLQGGAKRV
IISAPSADAPMFVMGVNHEKYDNSLKIISNASCTTNCLAPLAKVIHDNFGIVEGLMTTVH
AITATQKTVDGPSGKLWRDGRGALQNIIPASTGAAKAVGKVIPELNGKLTGMAFRVPTAN
VSVVDLTCRLEKPAKYDDIKKVVKQASEGPLKGILGYTEHQVVSSDFNSDTHSSTFDAGA
GIALNDHFVKLISWYDNEFGYSNRVVDLMAHMASKE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	5
F4F	(5aS,6R,9S,9aS)-9-methyl-9-oxidanyl-1-oxidanylidene-6-propan-2-yl-3,5a,6,7,8,9a…	C15 H22 O5	2
NAD	Nicotinamide-adenine-dinucleotide	C21 H27 N7 O14 P2	2

Water and common crystallization additives (EDO, PEG, GOL) are not listed.

Primary citation

Biosynthesis of the fungal glyceraldehyde-3-phosphate dehydrogenase inhibitor heptelidic acid and mechanism of self-resistance. Yan, Y., Zang, X., Cooper, S.J. et al. Chem Sci (2020) 11:9554-9562. DOI 10.1039/D0SC03805A

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
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
8G12 2.17 Å, CryoEM structure of nuclear GAPDH under 8h Oxidative Stress

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