3INM - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC NADP(+)-DEPENDENT ISOCITRATE DEHYDROGENASE R132H MUTANT IN COMPLEX WITH NADPH, ALPHA-KETOGLUTARATE AND CALCIUM(2+)

Authors :   E. Fontano, R. S. Brown, R. K. Suto, B. Bhyravbhatla

Date :   12 Aug 09 (Deposition) - 24 Nov 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C  (2x)

Keywords :   Rossmann Fold, Nadp, Ketoglutarate, Quaternary Complex, Oxidoreductase, Glyoxylate Bypass, Magnesium, Manganese, Metal- Binding, Peroxisome, Tricarboxylic Acid Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Dang, D. W. White, S. Gross, B. D. Bennett, M. A. Bittinger, E. M. Driggers, V. R. Fantin, H. G. Jang, S. Jin, M. C. Keenan, K. M. Marks R. M. Prins, P. S. Ward, K. E. Yen, L. M. Liau, J. D. Rabinowitz, L. C. Cantley, C. B. Thompson, M. G. Vander Heiden, S. M. Su
Cancer-Associated Idh1 Mutations Produce 2-Hydroxyglutarate
Nature V. 462 739 2009
PubMed-ID: 19935646 | Reference-DOI: 10.1038/NATURE08617

Molecule 1 - ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC
	Chains	:	A, B, C
	EC Number	:	1.1.1.42
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-41A(+)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	IDH1, PICD
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	IDH, CYTOSOLIC NADP-ISOCITRATE DEHYDROGENASE, OXALOSUCCINATE DECARBOXYLASE, NADP(+)-SPECIFIC ICDH, IDP

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 15)

No.	Name	Count	Type	Full Name
1	AKG	3	Ligand/Ion	2-OXOGLUTARIC ACID
2	CA	3	Ligand/Ion	CALCIUM ION
3	GOL	3	Ligand/Ion	GLYCEROL
4	NA	3	Ligand/Ion	SODIUM ION
5	NDP	3	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	AKG	2	Ligand/Ion	2-OXOGLUTARIC ACID
2	CA	-1	Ligand/Ion	CALCIUM ION
3	GOL	2	Ligand/Ion	GLYCEROL
4	NA	-1	Ligand/Ion	SODIUM ION
5	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	AKG	2	Ligand/Ion	2-OXOGLUTARIC ACID
2	CA	-1	Ligand/Ion	CALCIUM ION
3	GOL	2	Ligand/Ion	GLYCEROL
4	NA	-1	Ligand/Ion	SODIUM ION
5	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:72 , ALA A:74 , THR A:75 , THR A:77 , ARG A:82 , ASN A:96 , LEU A:288 , HIS A:309 , GLY A:310 , THR A:311 , VAL A:312 , THR A:313 , ARG A:314 , HIS A:315 , THR A:327 , ASN A:328 , HOH A:428 , HOH A:429 , HOH A:431 , HOH A:433 , HOH A:434 , HOH A:435 , HOH A:437 , HOH A:438 , AKG A:511 , NA A:522 , LEU B:250 , ASP B:253 , GLN B:257 , LYS B:260 , HOH B:426	BINDING SITE FOR RESIDUE NDP A 501
02	AC2	SOFTWARE	THR A:77 , SER A:94 , ASN A:96 , ARG A:100 , ARG A:109 , TYR A:139 , ASP A:275 , HOH A:431 , NDP A:501 , CA A:521 , LYS B:212 , ILE B:215 , ASP B:252	BINDING SITE FOR RESIDUE AKG A 511
03	AC3	SOFTWARE	ASP A:275 , ASP A:279 , HOH A:426 , HOH A:427 , AKG A:511 , ASP B:252	BINDING SITE FOR RESIDUE CA A 521
04	AC4	SOFTWARE	NDP A:501	BINDING SITE FOR RESIDUE NA A 522
05	AC5	SOFTWARE	GLN A:323 , GLU A:324 , THR A:325 , ASN A:393 , THR A:394 , PHE A:395	BINDING SITE FOR RESIDUE GOL A 531
06	AC6	SOFTWARE	PHE A:108 , ARG A:109 , GLU A:110 , MET A:199 , THR A:292	BINDING SITE FOR RESIDUE GOL A 532
07	AC7	SOFTWARE	ASP A:253 , GLN A:257 , LYS A:260 , LYS B:72 , ALA B:74 , THR B:75 , THR B:77 , ARG B:82 , ASN B:96 , ALA B:308 , HIS B:309 , GLY B:310 , THR B:311 , VAL B:312 , ARG B:314 , HIS B:315 , THR B:327 , ASN B:328 , HOH B:429 , HOH B:430 , HOH B:431 , HOH B:433 , HOH B:434 , HOH B:435 , HOH B:436 , AKG B:511 , NA B:522	BINDING SITE FOR RESIDUE NDP B 501
08	AC8	SOFTWARE	ASP A:252 , THR B:77 , SER B:94 , ASN B:96 , ARG B:100 , ARG B:109 , TYR B:139 , ASP B:275 , ALA B:308 , HOH B:431 , NDP B:501 , CA B:521	BINDING SITE FOR RESIDUE AKG B 511
09	AC9	SOFTWARE	ASP A:252 , ASP B:275 , ASP B:279 , HOH B:427 , HOH B:428 , AKG B:511	BINDING SITE FOR RESIDUE CA B 521
10	BC1	SOFTWARE	NDP B:501	BINDING SITE FOR RESIDUE NA B 522
11	BC2	SOFTWARE	ALA C:74 , THR C:75 , ILE C:76 , THR C:77 , ARG C:82 , ASN C:96 , LEU C:250 , ASP C:253 , GLN C:257 , LYS C:260 , LEU C:288 , ALA C:307 , ALA C:308 , HIS C:309 , GLY C:310 , THR C:311 , VAL C:312 , THR C:313 , ARG C:314 , HIS C:315 , ASN C:328 , HOH C:428 , HOH C:429 , HOH C:433 , HOH C:434 , HOH C:435 , HOH C:436 , HOH C:438 , AKG C:511 , NA C:522	BINDING SITE FOR RESIDUE NDP C 501
12	BC3	SOFTWARE	THR C:77 , SER C:94 , ASN C:96 , ARG C:100 , ARG C:109 , TYR C:139 , LYS C:212 , ILE C:215 , ASP C:252 , ASP C:275 , HOH C:431 , NDP C:501 , CA C:521	BINDING SITE FOR RESIDUE AKG C 511
13	BC4	SOFTWARE	ASP C:252 , ASP C:275 , ASP C:279 , HOH C:426 , HOH C:427 , AKG C:511	BINDING SITE FOR RESIDUE CA C 521
14	BC5	SOFTWARE	ARG C:314 , NDP C:501	BINDING SITE FOR RESIDUE NA C 522
15	BC6	SOFTWARE	PHE C:108 , GLU C:110 , ILE C:129 , MET C:199 , LYS C:203 , THR C:292	BINDING SITE FOR RESIDUE GOL C 532

(no "SS Bond" information available for 3INM)

(no "Cis Peptide Bond" information available for 3INM)

Asymmetric Unit (7, 21)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_036013	R	132	C	IDHC_HUMAN	Unclassified	121913499	A/B/C	H	132	C
2	CancerSNP	VAR_IDHC_HUMAN_CCDS2381_1_01 *	R	132	C	IDHC_HUMAN	Disease (Colorectal cancer)	---	A/B/C	H	132	C
3	UniProt	VAR_055454	R	132	G	IDHC_HUMAN	Unclassified	---	A/B/C	H	132	G
4	UniProt	VAR_055455	R	132	H	IDHC_HUMAN	Unclassified	121913500	A/B/C	H	132	H
5	UniProt	VAR_055456	R	132	L	IDHC_HUMAN	Unclassified	---	A/B/C	H	132	L
6	UniProt	VAR_055457	R	132	S	IDHC_HUMAN	Unclassified	121913499	A/B/C	H	132	S
7	UniProt	VAR_049780	V	178	I	IDHC_HUMAN	Polymorphism	34218846	A/B/C	V	178	I
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (7, 14)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_036013	R	132	C	IDHC_HUMAN	Unclassified	121913499	A/B	H	132	C
2	CancerSNP	VAR_IDHC_HUMAN_CCDS2381_1_01 *	R	132	C	IDHC_HUMAN	Disease (Colorectal cancer)	---	A/B	H	132	C
3	UniProt	VAR_055454	R	132	G	IDHC_HUMAN	Unclassified	---	A/B	H	132	G
4	UniProt	VAR_055455	R	132	H	IDHC_HUMAN	Unclassified	121913500	A/B	H	132	H
5	UniProt	VAR_055456	R	132	L	IDHC_HUMAN	Unclassified	---	A/B	H	132	L
6	UniProt	VAR_055457	R	132	S	IDHC_HUMAN	Unclassified	121913499	A/B	H	132	S
7	UniProt	VAR_049780	V	178	I	IDHC_HUMAN	Polymorphism	34218846	A/B	V	178	I
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (7, 14)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_036013	R	132	C	IDHC_HUMAN	Unclassified	121913499	C	H	132	C
2	CancerSNP	VAR_IDHC_HUMAN_CCDS2381_1_01 *	R	132	C	IDHC_HUMAN	Disease (Colorectal cancer)	---	C	H	132	C
3	UniProt	VAR_055454	R	132	G	IDHC_HUMAN	Unclassified	---	C	H	132	G
4	UniProt	VAR_055455	R	132	H	IDHC_HUMAN	Unclassified	121913500	C	H	132	H
5	UniProt	VAR_055456	R	132	L	IDHC_HUMAN	Unclassified	---	C	H	132	L
6	UniProt	VAR_055457	R	132	S	IDHC_HUMAN	Unclassified	121913499	C	H	132	S
7	UniProt	VAR_049780	V	178	I	IDHC_HUMAN	Polymorphism	34218846	C	V	178	I
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IDH_IMDH	PS00470	Isocitrate and isopropylmalate dehydrogenases signature.	IDHC_HUMAN	271-290	3	A:271-290 B:271-290 C:271-290

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IDH_IMDH	PS00470	Isocitrate and isopropylmalate dehydrogenases signature.	IDHC_HUMAN	271-290	2	A:271-290 B:271-290 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IDH_IMDH	PS00470	Isocitrate and isopropylmalate dehydrogenases signature.	IDHC_HUMAN	271-290	2	- - C:271-290

Asymmetric Unit (8, 24)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3a	ENST00000345146	3a	ENSE00001908890	chr2:209119857-209119663	195	IDHC_HUMAN	-	0	0	-	-
1.5d	ENST00000345146	5d	ENSE00001357891	chr2:209118683-209118610	74	IDHC_HUMAN	-	0	0	-	-
1.6a	ENST00000345146	6a	ENSE00002149609	chr2:209116291-209116154	138	IDHC_HUMAN	1-41	41	3	A:4-41 B:4-41 C:4-41	38 38 38
1.7c	ENST00000345146	7c	ENSE00000934687	chr2:209113384-209113093	292	IDHC_HUMAN	41-138	98	3	A:41-138 B:41-138 C:41-138	98 98 98
1.8b	ENST00000345146	8b	ENSE00002162985	chr2:209110148-209110043	106	IDHC_HUMAN	139-174	36	3	A:139-174 B:139-174 C:139-174	36 36 36
1.9b	ENST00000345146	9b	ENSE00001796387	chr2:209108328-209108151	178	IDHC_HUMAN	174-233	60	3	A:174-233 B:174-233 C:174-233	60 60 60
1.10	ENST00000345146	10	ENSE00000934684	chr2:209106869-209106718	152	IDHC_HUMAN	233-284	52	3	A:233-284 B:233-284 C:233-284	52 52 52
1.11b	ENST00000345146	11b	ENSE00000934683	chr2:209104727-209104587	141	IDHC_HUMAN	284-331	48	3	A:284-331 B:284-331 C:284-331	48 48 48
1.12	ENST00000345146	12	ENSE00000934682	chr2:209103957-209103795	163	IDHC_HUMAN	331-385	55	3	A:331-385 B:331-385 C:331-385	55 55 55
1.13f	ENST00000345146	13f	ENSE00000934681	chr2:209101893-209100951	943	IDHC_HUMAN	385-414	30	3	A:385-410 B:385-414 C:385-410	26 30 26

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:407
 aligned with IDHC_HUMAN | O75874 from UniProtKB/Swiss-Prot  Length:414

    Alignment length:407
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       
           IDHC_HUMAN     4 KISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLA 410
               SCOP domains d3inma_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 3inmA00 A:4-410 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.hhhhhhhhhhhhhhh....eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee................eeeeee..hhhhhheeeee...eeeeeeeee......eeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhh....eeeeee......eeeee....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------------------------------------------------------------------------------------------C---------------------------------------------I---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------------------------C-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) --------------------------------------------------------------------------------------------------------------------------------G-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
             SAPs(SNPs) (4) --------------------------------------------------------------------------------------------------------------------------------H-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (4)
             SAPs(SNPs) (5) --------------------------------------------------------------------------------------------------------------------------------L-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (5)
             SAPs(SNPs) (6) --------------------------------------------------------------------------------------------------------------------------------S-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (6)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.6a  PDB: A:4-41 UniProt: 1-41  -------------------------------------------------------------------------------------------------Exon 1.8b  PDB: A:139-174           ----------------------------------------------------------Exon 1.10  PDB: A:233-284 UniProt: 233-284          ----------------------------------------------Exon 1.12  PDB: A:331-385 UniProt: 331-385             ------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.7c  PDB: A:41-138 UniProt: 41-138                                                          -----------------------------------Exon 1.9b  PDB: A:174-233 UniProt: 174-233                  --------------------------------------------------Exon 1.11b  PDB: A:284-331 UniProt: 284-331     -----------------------------------------------------Exon 1.13f  PDB: A:385-410 Transcript 1 (2)
                 3inm A   4 KISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGHHAYGDQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLA 410
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403

Chain B from PDB  Type:PROTEIN  Length:411
 aligned with IDHC_HUMAN | O75874 from UniProtKB/Swiss-Prot  Length:414

    Alignment length:411
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413 
           IDHC_HUMAN     4 KISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKL 414
               SCOP domains d3inmb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 3inmB00 B:4-414 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.hhhhhhhhhhhhhhh....eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee................eeeeee..hhhhhheeeee...eeeeeeeee......eeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhh....eeeeee......eeee.....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------------------------------------------------------------------------------------------C---------------------------------------------I-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------------------------C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
             SAPs(SNPs) (3) --------------------------------------------------------------------------------------------------------------------------------G------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (3)
             SAPs(SNPs) (4) --------------------------------------------------------------------------------------------------------------------------------H------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (4)
             SAPs(SNPs) (5) --------------------------------------------------------------------------------------------------------------------------------L------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (5)
             SAPs(SNPs) (6) --------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (6)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ---------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6a  PDB: B:4-41 UniProt: 1-41  -------------------------------------------------------------------------------------------------Exon 1.8b  PDB: B:139-174           ----------------------------------------------------------Exon 1.10  PDB: B:233-284 UniProt: 233-284          ----------------------------------------------Exon 1.12  PDB: B:331-385 UniProt: 331-385             ----------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.7c  PDB: B:41-138 UniProt: 41-138                                                          -----------------------------------Exon 1.9b  PDB: B:174-233 UniProt: 174-233                  --------------------------------------------------Exon 1.11b  PDB: B:284-331 UniProt: 284-331     -----------------------------------------------------Exon 1.13f  PDB: B:385-414     Transcript 1 (2)
                 3inm B   4 KISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGHHAYGDQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKL 414
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413

Chain C from PDB  Type:PROTEIN  Length:407
 aligned with IDHC_HUMAN | O75874 from UniProtKB/Swiss-Prot  Length:414

    Alignment length:407
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       
           IDHC_HUMAN     4 KISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLA 410
               SCOP domains d3inmc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 3inmC00 C:4-410 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.hhhhhhhhhhhhhhh....eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhh.......hhhhhhhhhhh.eeeeee................eeeeee..hhhhhheeeee...eeeeeee........eeeeeeee....eeeee...hhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhh....eeeeee......eeee.....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------------------------------------------------------------------------------------------C---------------------------------------------I---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------------------------C-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) --------------------------------------------------------------------------------------------------------------------------------G-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
             SAPs(SNPs) (4) --------------------------------------------------------------------------------------------------------------------------------H-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (4)
             SAPs(SNPs) (5) --------------------------------------------------------------------------------------------------------------------------------L-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (5)
             SAPs(SNPs) (6) --------------------------------------------------------------------------------------------------------------------------------S-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (6)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.6a  PDB: C:4-41 UniProt: 1-41  -------------------------------------------------------------------------------------------------Exon 1.8b  PDB: C:139-174           ----------------------------------------------------------Exon 1.10  PDB: C:233-284 UniProt: 233-284          ----------------------------------------------Exon 1.12  PDB: C:331-385 UniProt: 331-385             ------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.7c  PDB: C:41-138 UniProt: 41-138                                                          -----------------------------------Exon 1.9b  PDB: C:174-233 UniProt: 174-233                  --------------------------------------------------Exon 1.11b  PDB: C:284-331 UniProt: 284-331     -----------------------------------------------------Exon 1.13f  PDB: C:385-410 Transcript 1 (2)
                 3inm C   4 KISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGHHAYGDQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLA 410
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Isocitrate/Isopropylmalate dehydrogenase-like (143)

Superfamily: Isocitrate/Isopropylmalate dehydrogenase-like (143)

Family: Dimeric isocitrate & isopropylmalate dehydrogenases (102)

Protein domain: automated matches (45)

Human (Homo sapiens) [TaxId: 9606] (7)

1a	d3inma_	A:
1b	d3inmc_	C:
1c	d3inmb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Isopropylmalate Dehydrogenase (91)

Homologous Superfamily: Isopropylmalate Dehydrogenase (91)

Human (Homo sapiens) (3)

1a	3inmA00	A:4-410
1b	3inmC00	C:4-410
1c	3inmB00	B:4-414

(no "Pfam Domain" information available for 3INM)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (IDHC_HUMAN | O75874)

molecular function
	GO:0051990	(R)-2-hydroxyglutarate dehydrogenase activity	Catalysis of the reaction: (R)-2-hydroxyglutarate + acceptor = 2-oxoglutarate + reduced acceptor.
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0050661	NADP binding	Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
	GO:0004450	isocitrate dehydrogenase (NADP+) activity	Catalysis of the reaction: isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH + H+.
	GO:0004448	isocitrate dehydrogenase activity	Catalysis of the reaction: isocitrate + acceptor = 2-oxoglutarate + CO2 + reduced acceptor.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
	GO:0006103	2-oxoglutarate metabolic process	The chemical reactions and pathways involving oxoglutarate, the dianion of 2-oxoglutaric acid. It is a key constituent of the TCA cycle and a key intermediate in amino-acid metabolism.
	GO:0006740	NADPH regeneration	A metabolic process that generates a pool of NADPH by the reduction of NADP+.
	GO:0008585	female gonad development	The process whose specific outcome is the progression of the female gonad over time, from its formation to the mature structure.
	GO:0006749	glutathione metabolic process	The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
	GO:0006097	glyoxylate cycle	A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.
	GO:0006102	isocitrate metabolic process	The chemical reactions and pathways involving isocitrate, the anion of isocitric acid, 1-hydroxy-1,2,3-propanetricarboxylic acid. Isocitrate is an important intermediate in the TCA cycle and the glycoxylate cycle.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0071071	regulation of phospholipid biosynthetic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of phospholipids.
	GO:0060696	regulation of phospholipid catabolic process	Any process that modulates the rate, frequency, or extent of phospholipid catabolism, the chemical reactions and pathways resulting in the breakdown of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
	GO:0014070	response to organic cyclic compound	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
	GO:0006979	response to oxidative stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0048545	response to steroid hormone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a steroid hormone stimulus.
	GO:0006099	tricarboxylic acid cycle	A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0005782	peroxisomal matrix	The volume contained within the membranes of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase.
	GO:0005777	peroxisome	A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		AKG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NDP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3inm)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3inm
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	IDHC_HUMAN \| O75874
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	1.1.1.42
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	IDHC_HUMAN \| O75874
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 3INM)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 15)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (7, 21)

PROSITE Motifs (1, 3)

Exons (8, 24)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (1, 3)

Pfam Domains (0, 0)

Gene Ontology (30, 30)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File