2R3E - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A RIBOKINASE-LIKE SUPERFAMILY PROTEIN (EF1790) FROM ENTEROCOCCUS FAECALIS V583 AT 1.95 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   29 Aug 07 (Deposition) - 11 Sep 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Putative Kinase In The Ribokinase-Like Superfamily, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Putative Kinase In The Ribokinase-Like Superfamily From Enterococcus Faecalis V583 (Np_815490. 1) At 1. 95 A Resolution
To Be Published
PubMed: search

Molecule 1 - YJEF-RELATED PROTEIN
	Atcc	:	700802
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	SPEEDET
	Expression System Strain	:	HK100
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NP_815490.1, EF_1790
	Organism Scientific	:	ENTEROCOCCUS FAECALIS
	Organism Taxid	:	226185
	Strain	:	V583

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 9)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	MSE	7	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 36)

No.	Name	Count	Type	Full Name
1	EDO	8	Ligand/Ion	1,2-ETHANEDIOL
2	MSE	28	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:35 , HOH A:370	BINDING SITE FOR RESIDUE EDO A 292
2	AC2	SOFTWARE	GLN A:177 , SER A:182 , THR A:183 , ALA A:196 , HOH A:382	BINDING SITE FOR RESIDUE EDO A 293

(no "SS Bond" information available for 2R3E)

(no "Cis Peptide Bond" information available for 2R3E)

(no "SAP(SNP)/Variant" information available for 2R3E)

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	YJEF_C_3	PS51383	YjeF C-terminal domain profile.	NNRD_ENTFA	5-273	1	A:5-273
2	YJEF_C_1	PS01049	YjeF C-terminal domain signature 1.	NNRD_ENTFA	95-105	1	A:95-105
3	YJEF_C_2	PS01050	YjeF C-terminal domain signature 2.	NNRD_ENTFA	212-222	1	A:212-222

Biological Unit 1 (3, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	YJEF_C_3	PS51383	YjeF C-terminal domain profile.	NNRD_ENTFA	5-273	4	A:5-273
2	YJEF_C_1	PS01049	YjeF C-terminal domain signature 1.	NNRD_ENTFA	95-105	4	A:95-105
3	YJEF_C_2	PS01050	YjeF C-terminal domain signature 2.	NNRD_ENTFA	212-222	4	A:212-222

(no "Exon" information available for 2R3E)

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:276
 aligned with NNRD_ENTFA | Q833Y3 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:276
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270      
           NNRD_ENTFA     1 MRYLSKDILEEVITQRPSDSYKSNFGRVVLIGGNRQYGGAIIMSTEACINSGAGLTTVITDVKNHGPLHARCPEAMVVGFEETVLLTNVVEQADVILIGPGLGLDATAQQILKMVLAQHQKQQWLIIDGSAITLFSQGNFSLTYPEKVVFTPHQMEWQRLSHLPIEQQTLANNQRQQAKLGSTIVLKSHRTTIFHAGEPFQNTGGNPGMATGGTGDTLAGIIAGFLAQFKPTIETIAGAVYLHSLIGDDLAKTDYVVLPTKISQALPTYMKKYAQP 276
               SCOP domains d2r3ea_ A: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -2r3eA00 A:2-276  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee.hhhhhhhhh.......hhhhh.eeeee.....hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh...eee...hhhhhhhhhhhh.eeee......hhhhhhhhhhhhhhh....eeeeehhhhhhhhhh.....hhh.eeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhh.eeee.....eee.....ee....hhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----YJEF_C_3  PDB: A:5-273 UniProt: 5-273                                                                                                                                                                                                                                        --- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------YJEF_C_1   ----------------------------------------------------------------------------------------------------------YJEF_C_2   ------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2r3e A   1 mRYLSKDILEEVITQRPSDSYKSNFGRVVLIGGNRQYGGAIImSTEACINSGAGLTTVITDVKNHGPLHARCPEAmVVGFEETVLLTNVVEQADVILIGPGLGLDATAQQILKmVLAQHQKQQWLIIDGSAITLFSQGNFSLTYPEKVVFTPHQmEWQRLSHLPIEQQTLANNQRQQAKLGSTIVLKSHRTTIFHAGEPFQNTGGNPGmATGGTGDTLAGIIAGFLAQFKPTIETIAGAVYLHSLIGDDLAKTDYVVLPTKISQALPTYmKKYAQP 276
                            |       10        20        30        40  |     50        60        70     |  80        90       100       110   |   120       130       140       150    |  160       170       180       190       200       210       220       230       240       250       260       270      
                            |                                        43-MSE                           76-MSE                               114-MSE                                  155-MSE                                               209-MSE                                                      270-MSE  
                            1-MSE

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: Ribokinase-like (226)

Superfamily: Ribokinase-like (189)

Family: automated matches (88)

Protein domain: automated matches (88)

Enterococcus faecalis [TaxId: 226185] (3)

d2r3ea_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (109)

Homologous Superfamily: [code=3.40.1190.20, no name defined] (73)

Enterococcus faecalis v583. Organism_taxid: 226185. Strain: v583. (2)

2r3eA00

A:2-276

(no "Pfam Domain" information available for 2R3E)

Asymmetric Unit(hide GO term definitions)

Chain A (NNRD_ENTFA | Q833Y3)

molecular function
	GO:0052855	ADP-dependent NAD(P)H-hydrate dehydratase activity	Catalysis of the reaction: (6S)-6beta-hydroxy-1,4,5,6-tetrahydronicotinamide adenine dinucleotide + ADP = AMP + 3 H(+) + NADH + phosphate.
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0046496	nicotinamide nucleotide metabolic process	The chemical reactions and pathways involving nicotinamide nucleotides, any nucleotide that contains combined nicotinamide.

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
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2r3e)

Biological Unit
	Complete Structure
		Biological Unit 1	[ 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 ](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
	2r3e
		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
	NNRD_ENTFA \| Q833Y3
		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
	NNRD_ENTFA \| Q833Y3
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	NNRD_ENTFA \| Q833Y3	:	2r3b

2r3b	CRYSTAL STRUCTURE OF A PUTATIVE KINASE IN THE RIBOKINASE- LIKE SUPERFAMILY FROM ENTEROCOCCUS FAECALIS V583 (NP_ 815490.1), ORTHORHOMBIC FORM.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 9)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

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