6DQG: Human glutamate dehydrogenase, H454Y mutant

Human glutamate dehydrogenase, H454Y mutant. Determined by X-ray diffraction at 2.7 Å resolution. Released 20 Jun 2018.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 6
Atoms: 23,591
Mol. weight: 332.24 kDa
Ligands: PO4
Released: 20 Jun 2018

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

Secondary structure: helices and β-sheets

6DQG contains 126 α-helices and 102 β-strands across 6 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.

Chains A, B, C and D: 21 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	15-33	19
α-helix	46-56	11
β-strand	61-70	10	1
β-strand	76-85	10	1
β-strand	93-96	4	2
β-strand	97-99	3	1
α-helix	105-121	17
β-strand	127-128	2	2
β-strand	129-133	5	1
α-helix	137-139	3
α-helix	142-158	17
β-strand	163	1	2
β-strand	167-170	4	2
α-helix	177-189	13
α-helix	198-201	4
α-helix	207-209	3
α-helix	218-231	14
α-helix	234-238	5
β-strand	250-254	5	3
α-helix	258-268	11
β-strand	273-278	6	3
β-strand	283-285	3	3
α-helix	292-301	10
β-strand	312-313	2	3
α-helix	318-320	3
β-strand	325-328	4	3
β-strand	335	1	4
α-helix	340-342	3
β-strand	347-349	3	3
β-strand	356	1	4
α-helix	358-366	9
β-strand	370-372	3	3
α-helix	374-377	4
α-helix	380-394	15
α-helix	403-424	22
α-helix	438-445	8
α-helix	449-474	26
α-helix	481-498	18

Chain E: 21 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	15-33	19
α-helix	46-56	11
β-strand	61-70	10	1
β-strand	76-85	10	1
β-strand	93-96	4	16
β-strand	97-99	3	1
α-helix	105-121	17
β-strand	127-128	2	16
β-strand	129-133	5	1
α-helix	137-139	3
α-helix	142-158	17
β-strand	163	1	16
β-strand	167-170	4	16
α-helix	177-189	13
α-helix	198-201	4
α-helix	207-209	3
α-helix	218-231	14
α-helix	234-238	5
β-strand	250-254	5	17
α-helix	258-269	12
β-strand	273-278	6	17
β-strand	283-285	3	17
α-helix	292-301	10
β-strand	312-313	2	17
α-helix	318-320	3
β-strand	325-328	4	17
β-strand	335	1	18
α-helix	340-342	3
β-strand	347-349	3	17
β-strand	356	1	18
α-helix	358-366	9
β-strand	370-372	3	17
α-helix	374-377	4
α-helix	380-394	15
α-helix	403-424	22
α-helix	438-445	8
α-helix	449-474	26
α-helix	481-498	18

Chain F: 21 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	15-33	19
α-helix	46-56	11
β-strand	61-70	10	9
β-strand	76-85	10	9
β-strand	93-96	4	19
β-strand	97-99	3	9
α-helix	105-121	17
β-strand	127-128	2	19
β-strand	129-133	5	9
α-helix	137-139	3
α-helix	142-159	18
β-strand	163	1	19
β-strand	167-170	4	19
α-helix	177-189	13
α-helix	198-201	4
α-helix	207-209	3
α-helix	218-231	14
α-helix	234-238	5
β-strand	250-254	5	20
α-helix	258-268	11
β-strand	273-278	6	20
β-strand	283-285	3	20
α-helix	292-301	10
β-strand	312-313	2	20
α-helix	318-320	3
β-strand	325-328	4	20
β-strand	335	1	21
α-helix	340-342	3
β-strand	347-349	3	20
β-strand	356	1	21
α-helix	358-366	9
β-strand	370-372	3	20
α-helix	374-377	4
α-helix	380-394	15
α-helix	403-424	22
α-helix	438-445	8
α-helix	449-474	26
α-helix	481-498	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate dehydrogenase 1, mitochondrial	A, B, C, D, E, F	protein	496	Homo sapiens	P00367 (AlphaFold model)

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

>6DQG_1 Glutamate dehydrogenase 1, mitochondrial (chains A, B, C, D, E, F)
DPNFFKMVEGFFDRGASIVEDKLVEDLRTRESEEQKRNRVRGILRIIKPCNHVLSLSFPI
RRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGA
KAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGIDVPAPDMSTGEREMSWIADTYAS
TIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIENFINEASYMSILGMTPGFGDK
TFVVQGFGNVGLHSMRYLHRFGAKCIAVGESDGSIWNPDGIDPKELEDFKLQHGSILGFP
KAKPYEGSILEADCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLERNI
MVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHG
GTIPIVPTAEFQDRISGASEKDIVYSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNA
IEKVFKVYNEAGVTFT

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	15

Primary citation

Glutamate dehydrogenase: Structure of a hyperinsulinism mutant, corrections to the atomic model, and insights into a regulatory site. Nassar, O.M., Li, C., Stanley, C.A. et al. Proteins (2019) 87:41-50. DOI 10.1002/prot.25620 · PubMed

Other PDB entries of the same protein (UniProt P00367 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8SK8 2.31 Å, human liver mitochondrial Glutamate dehydrogenase 1
8KGY 2.59 Å, Human glutamate dehydrogenase I
1L1F 2.7 Å, Structure of human glutamate dehydrogenase-apo form
8W4J 3.06 Å, Cryo-EM structure of the KLHL22 E3 ligase bound to human glutamate dehydrogenase I
7UZM 3.24 Å, Glutamate dehydrogenase 1 from human liver
1NR1 3.3 Å, Crystal structure of the R463A mutant of human Glutamate dehydrogenase

Browse structure collections

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