3DXF - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE HSCARG R37A MUTANT

Authors :   Y. Li, G. Meng, X. Dai, M. Luo, X. Zheng

Date :   24 Jul 08 (Deposition) - 12 May 09 (Release) - 12 May 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Rossmann Fold, Nadph-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Dai, Y. Li, G. Meng, S. Yao, Y. Zhao, Q. Yu, J. Zhang, M. Luo, X. Zheng
Nadph Is An Allosteric Regulator Of Hscarg
J. Mol. Biol. V. 387 1277 2009
PubMed-ID: 19254724 | Reference-DOI: 10.1016/J.JMB.2009.02.049
(for further references see the PDB file header)

Molecule 1 - NMRA-LIKE FAMILY DOMAIN-CONTAINING PROTEIN 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HSCARG PROTEIN

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3DXF)

(no "Site" information available for 3DXF)

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

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

Asymmetric Unit (2, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_030689	T	23	I	NMRL1_HUMAN	Polymorphism	11557236	A/B	T	23	I
2	UniProt	VAR_030690	P	252	L	NMRL1_HUMAN	Polymorphism	3747582	A	P	252	L

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

Biological Unit 1 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_030689	T	23	I	NMRL1_HUMAN	Polymorphism	11557236	A	T	23	I
2	UniProt	VAR_030690	P	252	L	NMRL1_HUMAN	Polymorphism	3747582	A	P	252	L

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_030689	T	23	I	NMRL1_HUMAN	Polymorphism	11557236	B	T	23	I

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

(no "PROSITE Motif" information available for 3DXF)

Asymmetric Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000283429	1a	ENSE00001526041	chr16:4524896-4524555	342	NMRL1_HUMAN	-	0	0	-	-
1.2	ENST00000283429	2	ENSE00001293533	chr16:4524167-4524094	74	NMRL1_HUMAN	1-14	14	2	A:4-14 B:4-14	11 11
1.3	ENST00000283429	3	ENSE00001010612	chr16:4519466-4519228	239	NMRL1_HUMAN	14-93	80	2	A:14-93 (gaps) B:14-93 (gaps)	80 80
1.4	ENST00000283429	4	ENSE00001010610	chr16:4516403-4516154	250	NMRL1_HUMAN	94-177	84	2	A:94-177 B:94-177	84 84
1.5	ENST00000283429	5	ENSE00001010609	chr16:4513851-4513661	191	NMRL1_HUMAN	177-240	64	2	A:177-240 B:177-240	64 64
1.6b	ENST00000283429	6b	ENSE00001900515	chr16:4511960-4511695	266	NMRL1_HUMAN	241-299	59	2	A:241-296 B:241-296 (gaps)	56 56

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:292
 aligned with NMRL1_HUMAN | Q9HBL8 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:293
                                    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   
          NMRL1_HUMAN     4 KKLVVVFGGTGAQGGSVARTLLEDGTFKVRVVTRNPRKKAAKELRLQGAEVVQGDQDDQVIMELALNGAYATFIVTNYWESCSQEQEVKQGKLLADLARRLGLHYVVYSGLENIKKLTAGRLAAAHFDGKGEVEEYFRDIGVPMTSVRLPCYFENLLSHFLPQKAPDGKSYLLSLPTGDVPMDGMSVSDLGPVVLSLLKMPEKYVGQNIGLSTCRHTAEEYAALLTKHTRKVVHDAKMTPEDYEKLGFPGARDLANMFRFYALRPDRDIELTLRLNPKALTLDQWLEQHKGDF 296
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhh.eeee....hhhhhhhhhh...eeee......-.hhhhhhhhhhhhhhhhhhh...eeee....hhhhhh.....hhhhhhhhhhhhhhhhh...eeeee..ee.hhhhh....ee......eee........eeeehhhhhhhhhhhhhhhhhhhh..eee...eeehhhhhhhhhhhhhh..eee...hhhhhhhhh..hhhhhhhhhhhhh.....hhhhhhhhh....hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------I------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L-------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2   -------------------------------------------------------------------------------Exon 1.4  PDB: A:94-177 UniProt: 94-177                                             ---------------------------------------------------------------Exon 1.6b  PDB: A:241-296 UniProt: 241-299 [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.3  PDB: A:14-93 (gaps) UniProt: 14-93                                    -----------------------------------------------------------------------------------Exon 1.5  PDB: A:177-240 UniProt: 177-240                       -------------------------------------------------------- Transcript 1 (2)
                 3dxf A   4 KKLVVVFGGTGAQGGSVARTLLEDGTFKVRVVTANPRKKAAKELRLQGAEVVQGDQDDQVIMELALNGAYATFIVTNYWE-CSQEQEVKQGKLLADLARRLGLHYVVYSGLENIKKLTAGRLAAAHFDGKGEVEEYFRDIGVPMTSVRLPCYFENLLSHFLPQKAPDGKSYLLSLPTGDVPMDGMSVSDLGPVVLSLLKMPEKYVGQNIGLSTCRHTAEEYAALLTKHTRKVVHDAKMTPEDYEKLGFPGARDLANMFRFYALRPDRDIELTLRLNPKALTLDQWLEQHKGDF 296
                                    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   
                                                                                                          83 |                                                                                                                                                                                                                   
                                                                                                            85

Chain B from PDB  Type:PROTEIN  Length:282
 aligned with NMRL1_HUMAN | Q9HBL8 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:293
                                    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   
          NMRL1_HUMAN     4 KKLVVVFGGTGAQGGSVARTLLEDGTFKVRVVTRNPRKKAAKELRLQGAEVVQGDQDDQVIMELALNGAYATFIVTNYWESCSQEQEVKQGKLLADLARRLGLHYVVYSGLENIKKLTAGRLAAAHFDGKGEVEEYFRDIGVPMTSVRLPCYFENLLSHFLPQKAPDGKSYLLSLPTGDVPMDGMSVSDLGPVVLSLLKMPEKYVGQNIGLSTCRHTAEEYAALLTKHTRKVVHDAKMTPEDYEKLGFPGARDLANMFRFYALRPDRDIELTLRLNPKALTLDQWLEQHKGDF 296
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhhh..eeeeee...--hhhhhhhhh..eeee....hhhhhhhhhh.eeeeee...-----hhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhh.....hhhhhhhhhhhhhhhhh...eeeee..ee.hhhhh....ee......eee........eeeehhhhhhhhhhhhhhhhhhhh..eee...eeehhhhhhhhhhhhhh..eee...hhhhhh...----hhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------I--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2   -------------------------------------------------------------------------------Exon 1.4  PDB: B:94-177 UniProt: 94-177                                             ---------------------------------------------------------------Exon 1.6b  PDB: B:241-296 (gaps) UniProt: 241-299        Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.3  PDB: B:14-93 (gaps) UniProt: 14-93                                    -----------------------------------------------------------------------------------Exon 1.5  PDB: B:177-240 UniProt: 177-240                       -------------------------------------------------------- Transcript 1 (2)
                 3dxf B   4 KKLVVVFGGTGAQGGSVARTLLEDGTFKVRVVTANP--KAAKELRLQGAEVVQGDQDDQVIMELALNGAYATFIVTN-----SQEQEVKQGKLLADLARRLGLHYVVYSGLENIKKLTAGRLAAAHFDGKGEVEEYFRDIGVPMTSVRLPCYFENLLSHFLPQKAPDGKSYLLSLPTGDVPMDGMSVSDLGPVVLSLLKMPEKYVGQNIGLSTCRHTAEEYAALLTKHTRKVVHDAKMTPEDYEKLG----RDLANMFRFYALRPDRDIELTLRLNPKALTLDQWLEQHKGDF 296
                                    13        23        33     |  43        53        63        73      |  -  |     93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243      |  - |     263       273       283       293   
                                                              39 42                                    80    86                                                                                                                                                                 250  255

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 '\|'

(no "SCOP Domain" information available for 3DXF)

(no "CATH Domain" information available for 3DXF)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (NMRL1_HUMAN | Q9HBL8)

biological process
	GO:0000050	urea cycle	The sequence of reactions by which arginine is synthesized from ornithine, then cleaved to yield urea and regenerate ornithine. The overall reaction equation is NH3 + CO2 + aspartate + 3 ATP + 2 H2O = urea + fumarate + 2 ADP + 2 phosphate + AMP + diphosphate.
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:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

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
(no "Ligands, Modified Residues, Ions" information available for 3dxf)

	Sites
(no "Sites" information available for 3dxf)

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

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 \| Biol. Unit 1 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
	3dxf
		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
	NMRL1_HUMAN \| Q9HBL8
		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)
	(no 'Enzyme Classificator' available)
		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
	NMRL1_HUMAN \| Q9HBL8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	NMRL1_HUMAN \| Q9HBL8	:	2exx 2wm3 2wmd 3e5m

2exx	THE WIDE-TYPE PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 3)

PROSITE Motifs (0, 0)

Exons (5, 10)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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