Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3INM

Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase R132H mutant in complex with NADPH, ALPHA-KETOGLUTARATE and CALCIUM(2+)

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0004450	molecular_function	isocitrate dehydrogenase (NADP+) activity
A	0005515	molecular_function	protein binding
A	0005576	cellular_component	extracellular region
A	0005737	cellular_component	cytoplasm
A	0005739	cellular_component	mitochondrion
A	0005777	cellular_component	peroxisome
A	0005782	cellular_component	peroxisomal matrix
A	0005829	cellular_component	cytosol
A	0006097	biological_process	glyoxylate cycle
A	0006099	biological_process	tricarboxylic acid cycle
A	0006102	biological_process	isocitrate metabolic process
A	0006103	biological_process	2-oxoglutarate metabolic process
A	0006739	biological_process	NADP+ metabolic process
A	0006740	biological_process	NADPH regeneration
A	0008585	biological_process	female gonad development
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	0034774	cellular_component	secretory granule lumen
A	0042802	molecular_function	identical protein binding
A	0042803	molecular_function	protein homodimerization activity
A	0045296	molecular_function	cadherin binding
A	0046872	molecular_function	metal ion binding
A	0048545	biological_process	response to steroid hormone
A	0050661	molecular_function	NADP binding
A	0051287	molecular_function	NAD binding
A	0070062	cellular_component	extracellular exosome
A	1904724	cellular_component	tertiary granule lumen
A	1904813	cellular_component	ficolin-1-rich granule lumen
B	0000287	molecular_function	magnesium ion binding
B	0004450	molecular_function	isocitrate dehydrogenase (NADP+) activity
B	0005515	molecular_function	protein binding
B	0005576	cellular_component	extracellular region
B	0005737	cellular_component	cytoplasm
B	0005739	cellular_component	mitochondrion
B	0005777	cellular_component	peroxisome
B	0005782	cellular_component	peroxisomal matrix
B	0005829	cellular_component	cytosol
B	0006097	biological_process	glyoxylate cycle
B	0006099	biological_process	tricarboxylic acid cycle
B	0006102	biological_process	isocitrate metabolic process
B	0006103	biological_process	2-oxoglutarate metabolic process
B	0006739	biological_process	NADP+ metabolic process
B	0006740	biological_process	NADPH regeneration
B	0008585	biological_process	female gonad development
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	0034774	cellular_component	secretory granule lumen
B	0042802	molecular_function	identical protein binding
B	0042803	molecular_function	protein homodimerization activity
B	0045296	molecular_function	cadherin binding
B	0046872	molecular_function	metal ion binding
B	0048545	biological_process	response to steroid hormone
B	0050661	molecular_function	NADP binding
B	0051287	molecular_function	NAD binding
B	0070062	cellular_component	extracellular exosome
B	1904724	cellular_component	tertiary granule lumen
B	1904813	cellular_component	ficolin-1-rich granule lumen
C	0000287	molecular_function	magnesium ion binding
C	0004450	molecular_function	isocitrate dehydrogenase (NADP+) activity
C	0005515	molecular_function	protein binding
C	0005576	cellular_component	extracellular region
C	0005737	cellular_component	cytoplasm
C	0005739	cellular_component	mitochondrion
C	0005777	cellular_component	peroxisome
C	0005782	cellular_component	peroxisomal matrix
C	0005829	cellular_component	cytosol
C	0006097	biological_process	glyoxylate cycle
C	0006099	biological_process	tricarboxylic acid cycle
C	0006102	biological_process	isocitrate metabolic process
C	0006103	biological_process	2-oxoglutarate metabolic process
C	0006739	biological_process	NADP+ metabolic process
C	0006740	biological_process	NADPH regeneration
C	0008585	biological_process	female gonad development
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	0034774	cellular_component	secretory granule lumen
C	0042802	molecular_function	identical protein binding
C	0042803	molecular_function	protein homodimerization activity
C	0045296	molecular_function	cadherin binding
C	0046872	molecular_function	metal ion binding
C	0048545	biological_process	response to steroid hormone
C	0050661	molecular_function	NADP binding
C	0051287	molecular_function	NAD binding
C	0070062	cellular_component	extracellular exosome
C	1904724	cellular_component	tertiary granule lumen
C	1904813	cellular_component	ficolin-1-rich granule lumen

Functional Information from PDB Data

site_id	AC1
Number of Residues	31
Details	BINDING SITE FOR RESIDUE NDP A 501

Chain	Residue
A	LYS72
A	THR311
A	VAL312
A	THR313
A	ARG314
A	HIS315
A	THR327
A	ASN328
A	HOH428
A	HOH429
A	HOH431
A	ALA74
A	HOH433
A	HOH434
A	HOH435
A	HOH437
A	HOH438
A	AKG511
A	NA522
B	LEU250
B	ASP253
B	GLN257
A	THR75
B	LYS260
B	HOH426
A	THR77
A	ARG82
A	ASN96
A	LEU288
A	HIS309
A	GLY310

site_id	AC2
Number of Residues	13
Details	BINDING SITE FOR RESIDUE AKG A 511

Chain	Residue
A	THR77
A	SER94
A	ASN96
A	ARG100
A	ARG109
A	TYR139
A	ASP275
A	HOH431
A	NDP501
A	CA521
B	LYS212
B	ILE215
B	ASP252

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA A 521

Chain	Residue
A	ASP275
A	ASP279
A	HOH426
A	HOH427
A	AKG511
B	ASP252

site_id	AC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NA A 522

Chain	Residue
A	NDP501

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 531

Chain	Residue
A	GLN323
A	GLU324
A	THR325
A	ASN393
A	THR394
A	PHE395

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 532

Chain	Residue
A	PHE108
A	ARG109
A	GLU110
A	MET199
A	THR292

site_id	AC7
Number of Residues	27
Details	BINDING SITE FOR RESIDUE NDP B 501

Chain	Residue
A	ASP253
A	GLN257
A	LYS260
B	LYS72
B	ALA74
B	THR75
B	THR77
B	ARG82
B	ASN96
B	ALA308
B	HIS309
B	GLY310
B	THR311
B	VAL312
B	ARG314
B	HIS315
B	THR327
B	ASN328
B	HOH429
B	HOH430
B	HOH431
B	HOH433
B	HOH434
B	HOH435
B	HOH436
B	AKG511
B	NA522

site_id	AC8
Number of Residues	12
Details	BINDING SITE FOR RESIDUE AKG B 511

Chain	Residue
B	NDP501
B	CA521
A	ASP252
B	THR77
B	SER94
B	ASN96
B	ARG100
B	ARG109
B	TYR139
B	ASP275
B	ALA308
B	HOH431

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA B 521

Chain	Residue
A	ASP252
B	ASP275
B	ASP279
B	HOH427
B	HOH428
B	AKG511

site_id	BC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NA B 522

Chain	Residue
B	NDP501

site_id	BC2
Number of Residues	30
Details	BINDING SITE FOR RESIDUE NDP C 501

Chain	Residue
C	ALA74
C	THR75
C	ILE76
C	THR77
C	ARG82
C	ASN96
C	LEU250
C	ASP253
C	GLN257
C	LYS260
C	LEU288
C	ALA307
C	ALA308
C	HIS309
C	GLY310
C	THR311
C	VAL312
C	THR313
C	ARG314
C	HIS315
C	ASN328
C	HOH428
C	HOH429
C	HOH433
C	HOH434
C	HOH435
C	HOH436
C	HOH438
C	AKG511
C	NA522

site_id	BC3
Number of Residues	13
Details	BINDING SITE FOR RESIDUE AKG C 511

Chain	Residue
C	THR77
C	SER94
C	ASN96
C	ARG100
C	ARG109
C	TYR139
C	LYS212
C	ILE215
C	ASP252
C	ASP275
C	HOH431
C	NDP501
C	CA521

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA C 521

Chain	Residue
C	ASP252
C	ASP275
C	ASP279
C	HOH426
C	HOH427
C	AKG511

site_id	BC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NA C 522

Chain	Residue
C	ARG314
C	NDP501

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL C 532

Chain	Residue
C	PHE108
C	GLU110
C	ILE129
C	MET199
C	LYS203
C	THR292

Functional Information from PROSITE/UniProt

site_id	PS00470
Number of Residues	20
Details	IDH_IMDH Isocitrate and isopropylmalate dehydrogenases signature. NYDGDVqSDsvAqgy.GSLGM

Chain	Residue	Details
A	ASN271-MET290

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"PubMed","id":"15173171","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19935646","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1T09","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1T0L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3INM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3MAP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3MAR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3MAS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4I3K","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4I3L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4KZO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4L03","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4L04","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4L06","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4UMX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4UMY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4XRX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4XS3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5DE1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5L57","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5L58","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5LGE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5SUN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5SVF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5TQH","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	27
Details	Binding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"15173171","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1T0L","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"15173171","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19935646","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1T09","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1T0L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3INM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3MAP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3MAR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3MAS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4I3K","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4I3L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4KZO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4L03","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4L04","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4L06","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4UMX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4UMY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4XRX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4XS3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5DE1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5L57","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5LGE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5SUN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5SVF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5TQH","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"15173171","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1T0L","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"15173171","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"19935646","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1T0L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3INM","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"15173171","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19935646","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1T0L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3INM","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	6
Details	Binding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"15173171","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"19935646","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1T0L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3INM","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	6
Details	Site: {"description":"Critical for catalysis"}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	3
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	12
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"O88844","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	6
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"O88844","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	3
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	3
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"O88844","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	1
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
A	THR155

site_id	CSA2
Number of Residues	1
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
B	THR155

site_id	CSA3
Number of Residues	1
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
C	THR155

site_id	CSA4
Number of Residues	2
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
A	LYS212
A	ASP252

site_id	CSA5
Number of Residues	2
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
B	LYS212
B	ASP252

site_id	CSA6
Number of Residues	2
Details	Annotated By Reference To The Literature 1a05

Chain	Residue	Details
C	LYS212
C	ASP252

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