Structure of PDB 2d4v Chain C

Receptor sequence

>2d4vC (length=427) Species: 930 (Acidithiobacillus thiooxidans)

THIQKPATGSPLTLLNGVLQVPDQPIIPFIEGDGIGCDVTPAMRSVVDAA
VAKVYGGQRQIAWMELFAGQKAVQLYGEGQYLPDETMAAIREYKVAIKGP
LETPVGGGIRSLNVAMRQDLDLYVCLRPVRYFEGTPSPMRHPEKVDMVIF
RENSEDIYAGIEWPAGSPEAEKIIRFLREEMGVTKIRFPDSSAIGIKPVS
TEGSERLIRRTIQYALEHGKPSVSLVHKGNIMKFTEGGFRDWGYALAERE
FAGRVFTWRQKAAISKAEGKAAGQKAEQQAIADGKLIIKDVIADNFLQQI
LLRPEDYSVVATLNLNGDYVSDALAAEVGGIGMAPGANLSDTHAIFEATH
GTAPDIAGQGKANPSSLILSAVMMLEHLGWGEAAQAIVAAMNATIAAGEV
TGDLAALRGDVPALSTTEFTAALIRRF

3D structure

• PDB: 2d4v Structure and quantum chemical analysis of NAD+-dependent isocitrate dehydrogenase: hydride transfer and co-factor specificity
• Chain: C
• Resolution: 1.9 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Y160 K230 D296 D320 D324
• Catalytic site (residue number reindexed from 1): Y158 K228 D294 D318 D322
• Enzyme Commision number: 1.1.1.42: isocitrate dehydrogenase (NADP(+)).

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	FLC	C	T105 S113 N115 R119 R129 R153 Y160 D320	T103 S111 N113 R117 R127 R151 Y158 D318
BS02	NAD	C	I37 P102 L103 E104 T105 N115 I333 E349 H352 G353 T354 A355 D357 A364 N365 D405	I35 P100 L101 E102 T103 N113 I331 E347 H350 G351 T352 A353 D355 A362 N363 D403
BS03	NAD	C	N232 I294 N297	N230 I292 N295

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0000287 magnesium ion binding
• GO:0004450 isocitrate dehydrogenase (NADP+) activity
• GO:0016491 oxidoreductase activity
• GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
• GO:0046872 metal ion binding
• GO:0051287 NAD binding

Biological Process

• GO:0006097 glyoxylate cycle
• GO:0006099 tricarboxylic acid cycle

External links

• PDB: RCSB:2d4v, PDBe:2d4v, PDBj:2d4v
• PDBsum: 2d4v
• PubMed: 17634983
• UniProt: Q8GAX0