PDB-6dhk: Bovine glutamate dehydrogenase complexed with ADP

ID or keywords:

Entry

Database: PDB / ID: 6dhk

Title

Bovine glutamate dehydrogenase complexed with ADP

Components

Glutamate dehydrogenase 1, mitochondrial

Keywords

OXIDOREDUCTASE /

Dehydrogenase /

glutamate /

ADP

Function / homology

Function and homology information

Glutamate and glutamine metabolism / Transcriptional activation of mitochondrial biogenesis / glutamate dehydrogenase [NAD(P)+] activity / glutamate catabolic process / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] /

glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / glutamine metabolic process / positive regulation of insulin secretion ...
Similarity search - Function

Biological species

Bos taurus (cattle)

Method

X-RAY DIFFRACTION / Resolution: 3.5 Å

Authors

Smith, T.J.

Citation

Journal: Biochemistry / Year: 2003
Title: Structural studies on ADP activation of mammalian glutamate dehydrogenase and the evolution of regulation.
Authors: Banerjee, S. / Schmidt, T. / Fang, J. / Stanley, C.A. / Smith, T.J.

History

Deposition	May 20, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 25, 2018	Provider: repository / Type: Initial release
Revision 1.1	Mar 13, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6dhk.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb6dhk.ent.gz	944.3 KB	Display	PDB format
PDBx/mmJSON format	6dhk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dh/6dhk ftp://data.pdbj.org/pub/pdb/validation_reports/dh/6dhk	HTTPS FTP

-
Related structure data

Related structure data	1nqtC 1nr1C 1nr7C C: citing same article (ref.)
Similar structure data	1nqt-2 1l1f-d 1nqt-1 3jcz-d 1nr1-d 1nr7-2 1nr7-1 3jd3-d 6dqg-d 3jd0-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#177 - Sep 2014 Apoptosomes similarity (1)

Deposited unit

A: Glutamate dehydrogenase 1, mitochondrial

B: Glutamate dehydrogenase 1, mitochondrial

C: Glutamate dehydrogenase 1, mitochondrial

D: Glutamate dehydrogenase 1, mitochondrial

E: Glutamate dehydrogenase 1, mitochondrial

F: Glutamate dehydrogenase 1, mitochondrial

G: Glutamate dehydrogenase 1, mitochondrial

H: Glutamate dehydrogenase 1, mitochondrial

I: Glutamate dehydrogenase 1, mitochondrial

J: Glutamate dehydrogenase 1, mitochondrial

K: Glutamate dehydrogenase 1, mitochondrial

L: Glutamate dehydrogenase 1, mitochondrial

hetero molecules

667 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glutamate dehydrogenase 1, mitochondrial

B: Glutamate dehydrogenase 1, mitochondrial

C: Glutamate dehydrogenase 1, mitochondrial

D: Glutamate dehydrogenase 1, mitochondrial

E: Glutamate dehydrogenase 1, mitochondrial

F: Glutamate dehydrogenase 1, mitochondrial

hetero molecules

defined by author&software
Evidence: equilibrium centrifugation, It is well known that GDH exists as a hexamer.
333 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: Glutamate dehydrogenase 1, mitochondrial

H: Glutamate dehydrogenase 1, mitochondrial

I: Glutamate dehydrogenase 1, mitochondrial

J: Glutamate dehydrogenase 1, mitochondrial

K: Glutamate dehydrogenase 1, mitochondrial

L: Glutamate dehydrogenase 1, mitochondrial

hetero molecules

defined by author&software
333 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	96.382, 172.160, 439.904
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	PHE	PHE	ILE	ILE	chain A and (resseq 10:212 )	A	A	10 - 212	5 - 207
2	1	PHE	PHE	ILE	ILE	chain B and (resseq 10:212 )	B	B	10 - 212	5 - 207
3	1	PHE	PHE	ILE	ILE	chain C and (resseq 10:212 )	C	C	10 - 212	5 - 207
4	1	PHE	PHE	ILE	ILE	chain D and (resseq 10:212 )	D	D	10 - 212	5 - 207
5	1	PHE	PHE	ILE	ILE	chain E and (resseq 10:212 )	E	E	10 - 212	5 - 207
6	1	PHE	PHE	ILE	ILE	chain F and (resseq 10:212 )	F	F	10 - 212	5 - 207
7	1	PHE	PHE	ILE	ILE	chain G and (resseq 10:212 )	G	G	10 - 212	5 - 207
8	1	PHE	PHE	ILE	ILE	chain H and (resseq 10:212 )	H	H	10 - 212	5 - 207
9	1	PHE	PHE	ILE	ILE	chain I and (resseq 10:212 )	I	I	10 - 212	5 - 207
10	1	PHE	PHE	ILE	ILE	chain J and (resseq 10:212 )	J	J	10 - 212	5 - 207
11	1	PHE	PHE	ILE	ILE	chain K and (resseq 10:212 )	K	K	10 - 212	5 - 207
12	1	PHE	PHE	ILE	ILE	chain L and (resseq 10:212 )	L	L	10 - 212	5 - 207
1	2	SER	SER	ARG	ARG	chain A and (resseq 213:396 )	A	A	213 - 396	208 - 391
2	2	SER	SER	ARG	ARG	chain B and (resseq 213:396 )	B	B	213 - 396	208 - 391
3	2	SER	SER	ARG	ARG	chain C and (resseq 213:396 )	C	C	213 - 396	208 - 391
4	2	SER	SER	ARG	ARG	chain D and (resseq 213:396 )	D	D	213 - 396	208 - 391
5	2	SER	SER	ARG	ARG	chain E and (resseq 213:396 )	E	E	213 - 396	208 - 391
6	2	SER	SER	ARG	ARG	chain F and (resseq 213:396 )	F	F	213 - 396	208 - 391
7	2	SER	SER	ARG	ARG	chain G and (resseq 213:396 )	G	G	213 - 396	208 - 391
8	2	SER	SER	ARG	ARG	chain H and (resseq 213:396 )	H	H	213 - 396	208 - 391
9	2	SER	SER	ARG	ARG	chain I and (resseq 213:396 )	I	I	213 - 396	208 - 391
10	2	SER	SER	ARG	ARG	chain J and (resseq 213:396 )	J	J	213 - 396	208 - 391
11	2	SER	SER	ARG	ARG	chain K and (resseq 213:396 )	K	K	213 - 396	208 - 391
12	2	SER	SER	ARG	ARG	chain L and (resseq 213:396 )	L	L	213 - 396	208 - 391
1	3	LEU	LEU	VAL	VAL	chain A and (resseq 397:449 )	A	A	397 - 449	392 - 444
2	3	LEU	LEU	VAL	VAL	chain B and (resseq 397:449 )	B	B	397 - 449	392 - 444
3	3	LEU	LEU	VAL	VAL	chain C and (resseq 397:449 )	C	C	397 - 449	392 - 444
4	3	LEU	LEU	VAL	VAL	chain D and (resseq 397:449 )	D	D	397 - 449	392 - 444
5	3	LEU	LEU	VAL	VAL	chain E and (resseq 397:449 )	E	E	397 - 449	392 - 444
6	3	LEU	LEU	VAL	VAL	chain F and (resseq 397:449 )	F	F	397 - 449	392 - 444
7	3	LEU	LEU	VAL	VAL	chain G and (resseq 397:449 )	G	G	397 - 449	392 - 444
8	3	LEU	LEU	VAL	VAL	chain H and (resseq 397:449 )	H	H	397 - 449	392 - 444
9	3	LEU	LEU	VAL	VAL	chain I and (resseq 397:449 )	I	I	397 - 449	392 - 444
10	3	LEU	LEU	VAL	VAL	chain J and (resseq 397:449 )	J	J	397 - 449	392 - 444
11	3	LEU	LEU	VAL	VAL	chain K and (resseq 397:449 )	K	K	397 - 449	392 - 444
12	3	LEU	LEU	VAL	VAL	chain L and (resseq 397:449 )	L	L	397 - 449	392 - 444

NCS ensembles :

ID
1
2
3

#1: Protein	Glutamate dehydrogenase 1, mitochondrial / Mass: 55127.648 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) References: UniProt: A0A140T871, UniProt: P00366*PLUS, glutamate dehydrogenase
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate Mass: 427.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.76 Å³/Da / Density % sol: 55.41 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: sodium phosphate, PEG8000, sodium azide, sodium chloride, MPD, OBG, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2000
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 3.5→30 Å / Num. obs: 90105 / % possible obs: 94 % / Redundancy: 3.1 % / Net I/σ(I): 14.7
Reflection shell	Resolution: 3.5→3.66 Å

-
Processing

Software

Name	Version	Classification
PHENIX	dev_1633	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Resolution: 3.5→29.935 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.94

	R_factor	Num. reflection	% reflection
R_free	0.2543	1999	2.2 %
R_work	0.2165	-	-
obs	0.2174	90940	97.52 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 3.5→29.935 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	46500	0	324	0	46824

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.026	47844
X-RAY DIFFRACTION	f_angle_d	2.783	64656
X-RAY DIFFRACTION	f_dihedral_angle_d	18.38	17808
X-RAY DIFFRACTION	f_chiral_restr	0.117	6996
X-RAY DIFFRACTION	f_plane_restr	0.012	8376

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	1587	X-RAY DIFFRACTION	POSITIONAL	0.214
1	2	B	1587	X-RAY DIFFRACTION	POSITIONAL	0.214
1	3	C	1587	X-RAY DIFFRACTION	POSITIONAL	0.19
1	4	D	1587	X-RAY DIFFRACTION	POSITIONAL	0.176
1	5	E	1587	X-RAY DIFFRACTION	POSITIONAL	0.204
1	6	F	1587	X-RAY DIFFRACTION	POSITIONAL	0.187
1	7	G	1587	X-RAY DIFFRACTION	POSITIONAL	0.188
1	8	H	1587	X-RAY DIFFRACTION	POSITIONAL	0.18
1	9	I	1587	X-RAY DIFFRACTION	POSITIONAL	0.195
1	10	J	1587	X-RAY DIFFRACTION	POSITIONAL	0.162
1	11	K	1587	X-RAY DIFFRACTION	POSITIONAL	0.179
1	12	L	1568	X-RAY DIFFRACTION	POSITIONAL	0.172
2	1	A	1413	X-RAY DIFFRACTION	POSITIONAL	0.219
2	2	B	1413	X-RAY DIFFRACTION	POSITIONAL	0.219
2	3	C	1413	X-RAY DIFFRACTION	POSITIONAL	0.222
2	4	D	1413	X-RAY DIFFRACTION	POSITIONAL	0.249
2	5	E	1413	X-RAY DIFFRACTION	POSITIONAL	0.234
2	6	F	1413	X-RAY DIFFRACTION	POSITIONAL	0.202
2	7	G	1413	X-RAY DIFFRACTION	POSITIONAL	0.204
2	8	H	1413	X-RAY DIFFRACTION	POSITIONAL	0.194
2	9	I	1413	X-RAY DIFFRACTION	POSITIONAL	0.218
2	10	J	1413	X-RAY DIFFRACTION	POSITIONAL	0.212
2	11	K	1413	X-RAY DIFFRACTION	POSITIONAL	0.214
2	12	L	1413	X-RAY DIFFRACTION	POSITIONAL	0.23
3	1	A	425	X-RAY DIFFRACTION	POSITIONAL	0.118
3	2	B	425	X-RAY DIFFRACTION	POSITIONAL	0.118
3	3	C	425	X-RAY DIFFRACTION	POSITIONAL	0.137
3	4	D	425	X-RAY DIFFRACTION	POSITIONAL	0.187
3	5	E	425	X-RAY DIFFRACTION	POSITIONAL	0.134
3	6	F	425	X-RAY DIFFRACTION	POSITIONAL	0.097
3	7	G	425	X-RAY DIFFRACTION	POSITIONAL	0.115
3	8	H	425	X-RAY DIFFRACTION	POSITIONAL	0.186
3	9	I	425	X-RAY DIFFRACTION	POSITIONAL	0.107
3	10	J	425	X-RAY DIFFRACTION	POSITIONAL	0.193
3	11	K	425	X-RAY DIFFRACTION	POSITIONAL	0.138
3	12	L	425	X-RAY DIFFRACTION	POSITIONAL	0.162

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.5-3.5874	0.3582	133	0.2871	5927	X-RAY DIFFRACTION	91
3.5874-3.6842	0.3072	141	0.2584	6273	X-RAY DIFFRACTION	98
3.6842-3.7924	0.2836	145	0.2455	6415	X-RAY DIFFRACTION	100
3.7924-3.9146	0.3052	143	0.2375	6419	X-RAY DIFFRACTION	100
3.9146-4.0542	0.2908	145	0.2321	6433	X-RAY DIFFRACTION	100
4.0542-4.2161	0.2755	145	0.2214	6409	X-RAY DIFFRACTION	99
4.2161-4.4074	0.2765	143	0.2158	6392	X-RAY DIFFRACTION	99
4.4074-4.6389	0.2118	142	0.188	6282	X-RAY DIFFRACTION	97
4.6389-4.9284	0.219	141	0.1876	6303	X-RAY DIFFRACTION	97
4.9284-5.307	0.2454	144	0.2098	6418	X-RAY DIFFRACTION	99
5.307-5.8375	0.2422	146	0.227	6463	X-RAY DIFFRACTION	99
5.8375-6.674	0.2651	146	0.2275	6494	X-RAY DIFFRACTION	99
6.674-8.3779	0.2724	144	0.2008	6450	X-RAY DIFFRACTION	97
8.3779-29.9364	0.195	141	0.1974	6263	X-RAY DIFFRACTION	91

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi