4WNI: Glyceraldehyde-3-phosphate dehydrogenase

Crystal structure of the T229K mutant of human GAPDH at 2.3 angstroems resolution. Determined by X-ray diffraction at 2.3 Å resolution. Released 3 Dec 2014.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,974
Mol. weight: 146.7 kDa
Ligands: ZN, NAD
Released: 3 Dec 2014

Explore 4WNI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4WNI contains 61 α-helices and 79 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 A: 15 helices, 20 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	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	109-114	6
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	152-167	16
β-strand	170-179	10	6
β-strand	186	1	7
α-helix	196-199	4
β-strand	201	1	7
β-strand	207-209	3	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 B: 16 helices, 20 β-strands

Element	Residues	Length	Sheet
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	109-114	6
β-strand	118-121	4	8
α-helix	129	1
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	255-266	12
β-strand	274-277	4	10
α-helix	283-286	4
β-strand	293-296	4	10
α-helix	297-299	3
β-strand	301-304	4	10
β-strand	307-314	8	10
α-helix	318-333	16

Chain C: 15 helices, 20 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
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	170-180	11	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	228-235	8	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	318-334	17

Chain O: 15 helices, 19 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	1
β-strand	66-69	4	1
β-strand	72-77	6	1
α-helix	82-84	3
α-helix	87-90	4
β-strand	94-97	4	1
α-helix	105-108	4
α-helix	109-114	6
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	152-167	16
β-strand	170-179	10	2
β-strand	186	1	3
α-helix	196-199	4
β-strand	201	1	3
β-strand	207-210	4	2
α-helix	213-220	8
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	293-296	4	2
β-strand	301-304	4	2
β-strand	307-314	8	2
α-helix	318-334	17

Molecules and chains

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

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

>4WNI_1 Glyceraldehyde-3-phosphate dehydrogenase (chains A, B, C, O)
MGKVKVGVNGFGRIGRLVTRAAFNSGKVDIVAINDPFIDLNYMVYMFQYDSTHGKFHGTV
KAENGKLVINGNPITIFQERDPSKIKWGDAGAEYVVESTGVFTTMEKAGAHLQGGAKRVI
ISAPSADAPMFVMGVNHEKYDNSLKIISNASCTTNCLAPLAKVIHDNFGIVEGLMTTVHA
ITATQKTVDGPSGKLWRDGRGALQNIIPASTGAAKAVGKVIPELNGKLKGMAFRVPTANV
SVVDLTCRLEKPAKYDDIKKVVKQASEGPLKGILGYTEHQVVSSDFNSDTHSSTFDAGAG
IALNDHFVKLISWYDNEFGYSNRVVDLMAHMASKE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3
NAD	Nicotinamide-adenine-dinucleotide	C21 H27 N7 O14 P2	3

Primary citation

A Dimer Interface Mutation in Glyceraldehyde-3-Phosphate Dehydrogenase Regulates Its Binding to AU-rich RNA. White, M.R., Khan, M.M., Deredge, D. et al. J Biol Chem (2015) 290:1770-1785. DOI 10.1074/jbc.M114.618165 · 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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