4L03 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE ANALYSIS OF HUMAN IDH1 MUTANTS IN COMPLEX WITH NADP+ AND CA2+/ALPHA-KETOGLUTARATE

Authors :   N. O. Concha, A. M. Smallwood

Date :   30 May 13 (Deposition) - 17 Jul 13 (Release) - 17 Jul 13 (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 :   Cytosolic, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. R. Rendina, B. Pietrak, A. Smallwood, H. Zhao, H. Qi, C. Quinn, N. D. Adams, N. Concha, C. Duraiswami, S. H. Thrall, S. Sweitzer, B. Schwartz
Mutant Idh1 Enhances The Production Of 2-Hydroxyglutarate Due To Its Kinetic Mechanism.
Biochemistry V. 52 4563 2013
PubMed-ID: 23731180 | Reference-DOI: 10.1021/BI400514K

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	:	PET41A
	Expression System Strain	:	ROSETTA 2(DE3)
	Expression System Taxid	:	562
	Gene	:	IDH1, PICD
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	IDH, CYTOSOLIC NADP-ISOCITRATE DEHYDROGENASE, IDP, NADP(+)- SPECIFIC ICDH, OXALOSUCCINATE DECARBOXYLASE

		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 (4, 10)

No.	Name	Count	Type	Full Name
1	AKG	3	Ligand/Ion	2-OXOGLUTARIC ACID
2	CA	3	Ligand/Ion	CALCIUM ION
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	NAP	3	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	AKG	2	Ligand/Ion	2-OXOGLUTARIC ACID
2	CA	-1	Ligand/Ion	CALCIUM ION
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	AKG	2	Ligand/Ion	2-OXOGLUTARIC ACID
2	CA	-1	Ligand/Ion	CALCIUM ION
3	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
4	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Asymmetric Unit (10, 10)

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 , ALA A:307 , ALA A:308 , HIS A:309 , GLY A:310 , THR A:311 , VAL A:312 , THR A:313 , ARG A:314 , HIS A:315 , ASN A:328 , AKG A:504 , HOH A:608 , HOH A:613 , HOH A:614 , HOH A:620 , HOH A:636 , HOH A:656 , HOH A:768 , HOH A:806 , HOH A:807 , LEU B:250 , ASP B:253 , GLN B:257 , LYS B:260 , HOH B:609 , HOH B:640	BINDING SITE FOR RESIDUE NAP A 501
02	AC2	SOFTWARE	ASP A:275 , ASP A:279 , AKG A:504 , HOH A:601 , HOH A:602 , ASP B:252	BINDING SITE FOR RESIDUE CA A 502
03	AC3	SOFTWARE	ASP A:273 , VAL A:276 , GLN A:277 , ASP B:273 , GLN B:277	BINDING SITE FOR RESIDUE EDO A 503
04	AC4	SOFTWARE	THR A:77 , SER A:94 , ASN A:96 , ARG A:100 , ARG A:109 , ARG A:132 , ASP A:275 , ALA A:308 , NAP A:501 , CA A:502 , HOH A:602 , HOH A:721 , LYS B:212 , ASP B:252 , HOH B:609	BINDING SITE FOR RESIDUE AKG A 504
05	AC5	SOFTWARE	LEU A:250 , ASP A:253 , GLN A:257 , LYS A:260 , HOH A:619 , HOH A:702 , HOH A:707 , LYS B:72 , ALA B:74 , THR B:75 , ILE B:76 , THR B:77 , ARG B:82 , ASN B:96 , ALA B:308 , HIS B:309 , GLY B:310 , THR B:311 , VAL B:312 , THR B:313 , ARG B:314 , HIS B:315 , ASN B:328 , AKG B:503 , HOH B:616 , HOH B:619 , HOH B:645 , HOH B:663 , HOH B:668 , HOH B:716 , HOH B:719 , HOH B:724 , HOH B:725	BINDING SITE FOR RESIDUE NAP B 501
06	AC6	SOFTWARE	ASP A:252 , ASP B:275 , ASP B:279 , AKG B:503 , HOH B:601 , HOH B:602	BINDING SITE FOR RESIDUE CA B 502
07	AC7	SOFTWARE	LYS A:212 , ASP A:252 , THR B:77 , SER B:94 , ASN B:96 , ARG B:100 , ARG B:109 , ARG B:132 , ASP B:275 , ALA B:308 , NAP B:501 , CA B:502 , HOH B:601 , HOH B:616 , HOH B:680 , HOH B:681	BINDING SITE FOR RESIDUE AKG B 503
08	AC8	SOFTWARE	LYS C:72 , ALA C:74 , THR C:75 , THR C:77 , ARG C:82 , ASN C:96 , LEU C:250 , ASP C:253 , GLN C:257 , LYS C:260 , 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 , AKG C:503 , HOH C:610 , HOH C:614 , HOH C:619 , HOH C:623 , HOH C:631 , HOH C:645 , HOH C:670 , HOH C:673 , HOH C:702 , HOH C:711	BINDING SITE FOR RESIDUE NAP C 501
09	AC9	SOFTWARE	ASP C:252 , ASP C:275 , ASP C:279 , AKG C:503 , HOH C:601 , HOH C:602	BINDING SITE FOR RESIDUE CA C 502
10	BC1	SOFTWARE	THR C:77 , SER C:94 , ASN C:96 , ARG C:100 , ARG C:109 , ARG C:132 , LYS C:212 , ILE C:215 , ASP C:252 , ASP C:275 , ALA C:308 , NAP C:501 , CA C:502 , HOH C:602 , HOH C:610 , HOH C:672 , HOH C:675	BINDING SITE FOR RESIDUE AKG C 503

(no "SS Bond" information available for 4L03)

(no "Cis Peptide Bond" information available for 4L03)

(no "SAP(SNP)/Variant" information available for 4L03)

(no "PROSITE Motif" information available for 4L03)

(no "Exon" information available for 4L03)

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:416
                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4l03a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.hhhhhhhhhhhhhhh....eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee................eeeeee..hhhhh.eeeee...eeeeeeeee......eeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhh.....eeeeee......eeee.....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l03 A   3 KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNDTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKLSLEH 418
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412

Chain B from PDB  Type:PROTEIN  Length:412
                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4l03b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.hhhhhhhhhhhhhhh....eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee................eeeeee..hhhhh.eeeee...eeeeeeeee......eeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhh.....eeeeee......eeee.....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l03 B   3 KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNDTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKL 414
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412

Chain C from PDB  Type:PROTEIN  Length:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4l03c_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.hhhhhhhhhhhhhhh....eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee................eeeeee..hhhhhheeeee...eeeeeee........eeeeeeee....eeeee...hhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhh.....eeeeee......eeee.....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l03 C   3 KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNDTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKLSLEHH 419
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412

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(

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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	d4l03a_	A:
1b	d4l03b_	B:
1c	d4l03c_	C:

(no "CATH Domain" information available for 4L03)

(no "Pfam Domain" information available for 4L03)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
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	4l03
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Description

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Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (30, 30)

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