1NR1: R463A mutant of human Glutamate dehydrogenase

Crystal structure of the R463A mutant of human Glutamate dehydrogenase. Determined by X-ray diffraction at 3.3 Å resolution. Released 6 May 2003.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 6
Atoms: 23,208
Mol. weight: 330.15 kDa
Released: 6 May 2003

Explore 1NR1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1NR1 contains 134 α-helices and 104 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.

Chain A: 24 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	13-37	25
α-helix	38-40	3
α-helix	42-44	3
α-helix	48-50	3
α-helix	51-56	6
β-strand	61-70	10	1
β-strand	76-85	10	1
β-strand	93-96	4	2
β-strand	97-98	2	1
α-helix	105-121	17
β-strand	127-128	2	2
β-strand	129-132	4	1
α-helix	137-139	3
α-helix	142-157	16
β-strand	163	1	2
β-strand	167-170	4	2
β-strand	172	1	3
β-strand	175	1	3
α-helix	177-189	13
α-helix	191-193	3
α-helix	198-200	3
α-helix	207-209	3
α-helix	215-231	17
α-helix	234-237	4
β-strand	250-253	4	4
α-helix	258-269	12
β-strand	273-277	5	4
β-strand	278	1	5
β-strand	283	1	5
α-helix	292-301	10
β-strand	325-327	3	4
β-strand	335	1	6
β-strand	347-349	3	4
β-strand	356	1	6
α-helix	358-366	9
β-strand	370-372	3	4
α-helix	374-377	4
α-helix	380-394	15
α-helix	403-421	19
α-helix	436-437	2
α-helix	438-445	8
α-helix	449-475	27
α-helix	481-498	18

Chain B: 23 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	13-37	25
α-helix	48-50	3
α-helix	51-56	6
β-strand	61-70	10	7
β-strand	76-85	10	7
β-strand	93-94	2	8
β-strand	97-98	2	7
α-helix	106-121	16
β-strand	127-128	2	8
β-strand	129-133	5	7
α-helix	137-139	3
α-helix	142-158	17
β-strand	163	1	8
β-strand	167-168	2	8
β-strand	172	1	9
β-strand	175	1	9
α-helix	177-189	13
α-helix	198-200	3
α-helix	207-209	3
α-helix	211-212	2
α-helix	218-231	14
α-helix	234-240	7
β-strand	250-254	5	10
α-helix	258-269	12
β-strand	273-278	6	10
β-strand	283	1	10
α-helix	292-301	10
α-helix	318-320	3
β-strand	325-328	4	10
β-strand	335	1	11
α-helix	340-342	3
β-strand	347-349	3	10
β-strand	356	1	11
α-helix	358-366	9
β-strand	370-372	3	10
α-helix	374-377	4
α-helix	380-394	15
α-helix	403-421	19
α-helix	438-446	9
α-helix	449-474	26
α-helix	481-498	18

Chain C: 23 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	13-37	25
α-helix	38-40	3
α-helix	51-56	6
β-strand	61-70	10	12
β-strand	76-85	10	12
β-strand	93-96	4	13
β-strand	97-98	2	12
α-helix	105-121	17
β-strand	127-128	2	13
β-strand	129-133	5	12
α-helix	137-139	3
α-helix	142-157	16
β-strand	167-170	4	13
α-helix	177-189	13
α-helix	198-201	4
α-helix	207-209	3
α-helix	215-231	17
α-helix	234-239	6
β-strand	250-254	5	14
α-helix	258-269	12
β-strand	273-278	6	14
β-strand	283	1	14
α-helix	292-301	10
α-helix	318-320	3
β-strand	325-328	4	14
β-strand	335	1	15
α-helix	340-342	3
β-strand	347-349	3	14
β-strand	356	1	15
α-helix	358-366	9
β-strand	370-372	3	14
α-helix	374-377	4
α-helix	380-394	15
α-helix	403-421	19
α-helix	436-437	2
α-helix	438-445	8
α-helix	449-475	27
α-helix	481-498	18

Chain D: 18 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	13-37	25
α-helix	38-40	3
α-helix	51-56	6
β-strand	61-70	10	7
β-strand	76-85	10	7
β-strand	93-96	4	16
β-strand	97-98	2	7
α-helix	105-119	15
β-strand	128	1	16
β-strand	129-132	4	7
α-helix	142-159	18
β-strand	163	1	16
β-strand	167-170	4	16
β-strand	172	1	17
β-strand	175	1	17
α-helix	177-189	13
α-helix	198-201	4
α-helix	218-231	14
β-strand	250-254	5	18
α-helix	258-269	12
β-strand	273-277	5	18
β-strand	284	1	18
α-helix	292-300	9
β-strand	325-328	4	18
β-strand	335	1	19
α-helix	340-342	3
β-strand	347-349	3	18
β-strand	356	1	19
α-helix	358-366	9
β-strand	370-372	3	18
α-helix	374-377	4
α-helix	381-394	14
α-helix	403-422	20
α-helix	438-444	7
α-helix	450-474	25
α-helix	481-498	18

Chain E: 22 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	13-37	25
α-helix	48-51	4
α-helix	52-56	5
β-strand	61-65	5	1
β-strand	67-69	3	20
β-strand	77-79	3	20
β-strand	81-85	5	1
β-strand	93-96	4	21
β-strand	97-99	3	1
α-helix	105-121	17
β-strand	127-128	2	21
β-strand	129-133	5	1
α-helix	142-158	17
β-strand	167-170	4	21
α-helix	177-189	13
α-helix	198-200	3
α-helix	207-209	3
α-helix	215-231	17
α-helix	234-239	6
β-strand	250-254	5	22
α-helix	258-269	12
β-strand	273-278	6	22
β-strand	283	1	22
α-helix	292-301	10
α-helix	312-313	2
β-strand	314	1	22
α-helix	318-320	3
β-strand	325-328	4	22
β-strand	335	1	23
α-helix	340-342	3
β-strand	347-349	3	22
β-strand	356	1	23
α-helix	358-366	9
β-strand	370-372	3	22
α-helix	374-377	4
α-helix	380-394	15
α-helix	403-421	19
α-helix	438-446	9
α-helix	449-474	26
α-helix	481-498	18

Chain F: 24 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	13-32	20
α-helix	33-37	5
α-helix	38-40	3
α-helix	42-44	3
α-helix	52-56	5
β-strand	61-70	10	12
β-strand	76-85	10	12
β-strand	93-94	2	24
β-strand	97-100	4	12
α-helix	105-121	17
β-strand	127-128	2	24
β-strand	129-134	6	12
α-helix	137-139	3
α-helix	142-159	18
β-strand	167-168	2	24
α-helix	177-188	12
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	25
α-helix	258-269	12
β-strand	273-278	6	25
β-strand	283	1	25
α-helix	292-301	10
α-helix	318-320	3
β-strand	325-328	4	25
β-strand	335	1	26
α-helix	340-342	3
β-strand	347-349	3	25
β-strand	356	1	26
α-helix	358-366	9
β-strand	370-372	3	25
α-helix	374-377	4
α-helix	380-394	15
α-helix	403-421	19
α-helix	438-445	8
α-helix	449-474	26
β-strand	480	1	25
α-helix	481-498	18

Molecules and chains

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

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

>1NR1_1 Glutamate dehydrogenase 1 (chains A, B, C, D, E, F)
DPNFFKMVEGFFDRGASIVEDKLVEDLRTRESEEQKRNRVRGILRIIKPCNHVLSLSFPI
RRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGA
KAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGIDVPAPDMSTGEREMSWIADTYAS
TIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIENFINEASYMSILGMTPGFGDK
TFVVQGFGNVGLHSMRYLHRFGAKCIAVGESDGSIWNPDGIDPKELEDFKLQHGSILGFP
KAKPYEGSILEADCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLERNI
MVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHG
GTIPIVPTAEFQDRISGASEKDIVHSGLAYTMEASARQIMRTAMKYNLGLDLRTAAYVNA
IEKVFKVYNEAGVTFT

Primary citation

Structural studies on ADP activation of mammalian glutamate dehydrogenase and the evolution of regulation. Banerjee, S., Schmidt, T., Fang, J. et al. Biochemistry (2003) 42:3446-3456. DOI 10.1021/bi0206917 · 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
6DQG 2.7 Å, Human glutamate dehydrogenase, H454Y mutant
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

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