Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3R8W

Structure of 3-isopropylmalate dehydrogenase isoform 2 from Arabidopsis thaliana at 2.2 angstrom resolution

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0003862	molecular_function	3-isopropylmalate dehydrogenase activity
A	0005829	cellular_component	cytosol
A	0008652	biological_process	amino acid biosynthetic process
A	0009082	biological_process	branched-chain amino acid biosynthetic process
A	0009098	biological_process	L-leucine biosynthetic process
A	0009507	cellular_component	chloroplast
A	0009536	cellular_component	plastid
A	0009553	biological_process	embryo sac development
A	0009555	biological_process	pollen development
A	0009570	cellular_component	chloroplast stroma
A	0009941	cellular_component	chloroplast envelope
A	0016491	molecular_function	oxidoreductase activity
A	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
A	0042803	molecular_function	protein homodimerization activity
A	0046872	molecular_function	metal ion binding
A	0051287	molecular_function	NAD binding
A	0070403	molecular_function	NAD+ binding
B	0000287	molecular_function	magnesium ion binding
B	0003862	molecular_function	3-isopropylmalate dehydrogenase activity
B	0005829	cellular_component	cytosol
B	0008652	biological_process	amino acid biosynthetic process
B	0009082	biological_process	branched-chain amino acid biosynthetic process
B	0009098	biological_process	L-leucine biosynthetic process
B	0009507	cellular_component	chloroplast
B	0009536	cellular_component	plastid
B	0009553	biological_process	embryo sac development
B	0009555	biological_process	pollen development
B	0009570	cellular_component	chloroplast stroma
B	0009941	cellular_component	chloroplast envelope
B	0016491	molecular_function	oxidoreductase activity
B	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
B	0042803	molecular_function	protein homodimerization activity
B	0046872	molecular_function	metal ion binding
B	0051287	molecular_function	NAD binding
B	0070403	molecular_function	NAD+ binding
C	0000287	molecular_function	magnesium ion binding
C	0003862	molecular_function	3-isopropylmalate dehydrogenase activity
C	0005829	cellular_component	cytosol
C	0008652	biological_process	amino acid biosynthetic process
C	0009082	biological_process	branched-chain amino acid biosynthetic process
C	0009098	biological_process	L-leucine biosynthetic process
C	0009507	cellular_component	chloroplast
C	0009536	cellular_component	plastid
C	0009553	biological_process	embryo sac development
C	0009555	biological_process	pollen development
C	0009570	cellular_component	chloroplast stroma
C	0009941	cellular_component	chloroplast envelope
C	0016491	molecular_function	oxidoreductase activity
C	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
C	0042803	molecular_function	protein homodimerization activity
C	0046872	molecular_function	metal ion binding
C	0051287	molecular_function	NAD binding
C	0070403	molecular_function	NAD+ binding
D	0000287	molecular_function	magnesium ion binding
D	0003862	molecular_function	3-isopropylmalate dehydrogenase activity
D	0005829	cellular_component	cytosol
D	0008652	biological_process	amino acid biosynthetic process
D	0009082	biological_process	branched-chain amino acid biosynthetic process
D	0009098	biological_process	L-leucine biosynthetic process
D	0009507	cellular_component	chloroplast
D	0009536	cellular_component	plastid
D	0009553	biological_process	embryo sac development
D	0009555	biological_process	pollen development
D	0009570	cellular_component	chloroplast stroma
D	0009941	cellular_component	chloroplast envelope
D	0016491	molecular_function	oxidoreductase activity
D	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
D	0042803	molecular_function	protein homodimerization activity
D	0046872	molecular_function	metal ion binding
D	0051287	molecular_function	NAD binding
D	0070403	molecular_function	NAD+ binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT A 368

Chain	Residue
A	LYS151
A	PHE161
B	GLU146

site_id	AC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACT A 369

Chain	Residue
A	HIS169
A	ARG173

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACT A 370

Chain	Residue
A	GLU91
A	ARG98
A	ARG108
A	ARG136

site_id	AC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACT A 371

Chain	Residue
A	ASP235
A	GLN238

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACT A 372

Chain	Residue
A	ILE15
A	ASN296
A	ASP337
A	HOH487

site_id	AC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACT B 368

Chain	Residue
B	HIS169
B	ARG173

site_id	AC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACT B 369

Chain	Residue
B	ASP235
B	GLN238

site_id	AC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACT B 370

Chain	Residue
B	ASP254
B	ILE282

site_id	AC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACT B 371

Chain	Residue
B	ASN296
B	ASP337

site_id	BC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE ACT B 372

Chain	Residue
B	ARG207

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACT B 373

Chain	Residue
B	GLU91
B	ARG98
B	ARG108
B	ARG136

site_id	BC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT C 368

Chain	Residue
C	ARG98
C	ARG108
C	ARG136

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACT D 368

Chain	Residue
D	GLU91
D	ARG98
D	ARG108
D	ARG136

site_id	BC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT D 369

Chain	Residue
D	ASP235
D	LYS237
D	GLN238

site_id	BC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACT D 370

Chain	Residue
D	ARG108
D	ASP254

Functional Information from PROSITE/UniProt

site_id	PS00470
Number of Residues	20
Details	IDH_IMDH Isocitrate and isopropylmalate dehydrogenases signature. NIFGDIlSDeaSmit.GSIGM

Chain	Residue	Details
A	ASN246-MET265

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	132
Details	Binding site: {"evidences":[{"source":"PubMed","id":"27137927","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5J33","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	16
Details	Binding site: {"evidences":[{"source":"PubMed","id":"27137927","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5J32","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"27137927","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5J32","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5J33","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5J34","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Site: {"description":"Confers substrate specificity","evidences":[{"source":"PubMed","id":"21697089","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	8
Details	Site: {"description":"Important for catalysis","evidences":[{"source":"PubMed","id":"27137927","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	8
Details	Site: {"description":"Essential for redox regulation","evidences":[{"source":"UniProtKB","id":"Q9FMT1","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q9FMT1","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)