Structure of PDB 3jd4 Chain D

Receptor sequence
>3jd4D (length=497) Species: 9913 (Bos taurus) [Search protein sequence]
DDPNFFKMVEGFFDRGASIVEDKLVEDLKTRETEEQKRNRVRSILRIIKP
CNHVLSLSFPIRRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEV
KALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELAK
KGFIGPGVDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPIS
QGGIHGRISATGRGVFHGIENFINEASYMSILGMTPGFGDKTFVVQGFGN
VGLHSMRYLHRFGAKCITVGESDGSIWNPDGIDPKELEDFKLQHGTILGF
PKAKIYEGSILEVDCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTP
EADKIFLERNIMVIPDLYLNAGGVTVSYFEWLNNLNHVSYGRLTFKYERD
SNYHLLMSVQESLERKFGKHGGTIPIVPTAEFQDRISGASEKDIVHSGLA
YTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKVFRVYNEAGVTFT
3D structure
PDB3jd4 Using Cryo-EM to Map Small Ligands on Dynamic Metabolic Enzymes: Studies with Glutamate Dehydrogenase.
ChainD
Resolution3.4 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Catalytic site (original residue number in PDB) K126 D168
Catalytic site (residue number reindexed from 1) K122 D164
Enzyme Commision number 1.4.1.3: glutamate dehydrogenase [NAD(P)(+)].
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 NAI D M169 G253 N254 V255 E275 S276 A326 N349 M165 G249 N250 V251 E271 S272 A322 N345
BS02 GTP D H209 S213 R261 Y262 E292 H450 H205 S209 R257 Y258 E288 H446
BS03 NAI D H195 Q205 G206 N388 H391 H191 Q201 G202 N384 H387
BS04 NAI D H85 R86 C115 D119 V120 K488 H81 R82 C111 D115 V116 K484
Gene Ontology
Molecular Function
GO:0004352 glutamate dehydrogenase (NAD+) activity
GO:0004353 glutamate dehydrogenase [NAD(P)+] activity
GO:0004354 glutamate dehydrogenase (NADP+) activity
GO:0005524 ATP binding
GO:0005525 GTP binding
GO:0016491 oxidoreductase activity
GO:0016639 oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor
GO:0042802 identical protein binding
Biological Process
GO:0006520 amino acid metabolic process
GO:0006538 glutamate catabolic process
GO:0006541 glutamine metabolic process
GO:0072350 tricarboxylic acid metabolic process
Cellular Component
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005783 endoplasmic reticulum

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3jd4, PDBe:3jd4, PDBj:3jd4
PDBsum3jd4
PubMed27036132
UniProtP00366|DHE3_BOVIN Glutamate dehydrogenase 1, mitochondrial (Gene Name=GLUD1)

[Back to BioLiP]