5ELM - JenaLib

Title :   CRYSTAL STRUCTURE OF L-ASPARTATE/GLUTAMATE SPECIFIC RACEMASE IN COMPLEX WITH L-GLUTAMATE

Authors :   J. W. Ahn, J. H. Chang, K. J. Kim

Date :   04 Nov 15 (Deposition) - 18 Nov 15 (Release) - 13 Jan 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Asp/Glu Racemase, L-Form Specific Racemase, Amino Acid Enantiomers, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. W. Ahn, J. H. Chang, K. J. Kim
Structural Basis For An Atypical Active Site Of An L-Aspartate/Glutamate-Specific Racemase From Escherichia Coli
Febs Lett. V. 589 3842 2015
PubMed-ID: 26555188 | Reference-DOI: 10.1016/J.FEBSLET.2015.11.003

Compounds

Molecule 1 - ASP/GLU_RACEMASE FAMILY PROTEIN
	Chains	:	A, B, C, D
	EC Number	:	5.1.1.13
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30A(+)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	ASPARTATE RACEMASE,PUTATIVE RACEMASE,PUTATIVE RESISTANCE PROTEINS,RACEMASE,STRAIN O157 SVETEC SCAFFOLD16.1,WHOLE GENOME SHOTGUN SEQUENCE

Structural Features

Chains, Units

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 6)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	GLU	3	Mod. Amino Acid	GLUTAMIC ACID
2	GOL	2	Ligand/Ion	GLYCEROL
3	NO3	1	Ligand/Ion	NITRATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	GLU	1	Mod. Amino Acid	GLUTAMIC ACID
2	GOL	1	Ligand/Ion	GLYCEROL
3	NO3	-1	Ligand/Ion	NITRATE ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	GLU	2	Mod. Amino Acid	GLUTAMIC ACID
2	GOL	1	Ligand/Ion	GLYCEROL
3	NO3	1	Ligand/Ion	NITRATE ION

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:409 , HOH A:415	binding site for residue GOL A 301
2	AC2	SOFTWARE	MET B:10 , PHE B:45 , GLN B:52 , THR B:83 , ASN B:84 , THR B:85 , PHE B:162 , SER B:197 , THR B:198 , GLU B:199 , HOH B:405	binding site for residue GLU B 301
3	AC3	SOFTWARE	MET C:10 , PHE C:45 , THR C:83 , ASN C:84 , THR C:85 , THR C:125 , PHE C:162 , SER C:197 , THR C:198 , GLU C:199 , HOH C:435	binding site for residue GLU C 301
4	AC4	SOFTWARE	MET D:10 , PHE D:45 , GLN D:52 , THR D:83 , ASN D:84 , THR D:85 , MET D:86 , PHE D:162 , SER D:197 , THR D:198 , GLU D:199	binding site for residue GLU D 301
5	AC5	SOFTWARE	ARG D:29 , LEU D:30 , HOH D:436 , HOH D:491	binding site for residue NO3 D 302
6	AC6	SOFTWARE	THR B:118 , ARG B:119 , HOH B:411 , PHE D:101 , LEU D:102 , HIS D:103 , ASP D:106 , ARG D:110 , ASP D:223	binding site for residue GOL D 303

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:235
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhh.....hhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhh.eee..hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhh...eeehhhhhhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5elm A   1 MKTIGLLGGMSWESTIPYYRLINEGIKQRLGGLHSAQVLLHSVDFHEIEECQRRGEWDKTGDILAEAALGLQRAGAEGIVLCTNTMHKVADAIESRCTLPFLHIADATGRAITGAGMTRVALLGTRYTMEQDFYRGRLTEQFSINCLIPEADERAKINQIIFEELCLGQFTEASRAYYAQVIARLAEQGAQGVIFGSTEIGLLVPEERSVLPVFDTAAIHAEDAVAFMLSLEHHH 235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain B from PDB  Type:PROTEIN  Length:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhh.....hhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhh.eee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....eee.........hhhhh...eeehhhhhhhhhhhhhh.hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5elm B   1 MKTIGLLGGMSWESTIPYYRLINEGIKQRLGGLHSAQVLLHSVDFHEIEECQRRGEWDKTGDILAEAALGLQRAGAEGIVLCTNTMHKVADAIESRCTLPFLHIADATGRAITGAGMTRVALLGTRYTMEQDFYRGRLTEQFSINCLIPEADERAKINQIIFEELCLGQFTEASRAYYAQVIARLAEQGAQGVIFGSTEIGLLVPEERSVLPVFDTAAIHAEDAVAFMLSLEHHHE 301
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    ||
                                                                                                                                                                                                                                                                    235|
                                                                                                                                                                                                                                                                     301

Chain C from PDB  Type:PROTEIN  Length:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee..hhhhhhhhhhhhhh.....hhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhh.eee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh......eee...hhhhhh........eeehhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5elm C   1 MKTIGLLGGMSWESTIPYYRLINEGIKQRLGGLHSAQVLLHSVDFHEIEECQRRGEWDKTGDILAEAALGLQRAGAEGIVLCTNTMHKVADAIESRCTLPFLHIADATGRAITGAGMTRVALLGTRYTMEQDFYRGRLTEQFSINCLIPEADERAKINQIIFEELCLGQFTEASRAYYAQVIARLAEQGAQGVIFGSTEIGLLVPEERSVLPVFDTAAIHAEDAVAFMLSLEHHHE 301
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    ||
                                                                                                                                                                                                                                                                    235|
                                                                                                                                                                                                                                                                     301

Chain D from PDB  Type:PROTEIN  Length:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhh.....hhhhhhhhhhhhh...eeeee.hhhhhhh..hhhhhhhhhh.eee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....eee...hhhhhhhhhhh...eeehhhhhhhhhhhhhh.hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5elm D   1 MKTIGLLGGMSWESTIPYYRLINEGIKQRLGGLHSAQVLLHSVDFHEIEECQRRGEWDKTGDILAEAALGLQRAGAEGIVLCTNTMHKVADAIESRCTLPFLHIADATGRAITGAGMTRVALLGTRYTMEQDFYRGRLTEQFSINCLIPEADERAKINQIIFEELCLGQFTEASRAYYAQVIARLAEQGAQGVIFGSTEIGLLVPEERSVLPVFDTAAIHAEDAVAFMLSLEHHHE 301
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    ||
                                                                                                                                                                                                                                                                    235|
                                                                                                                                                                                                                                                                     301

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

Visualization

Interactive Views

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
		GLU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NO3	[ 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 ]

	Cis Peptide Bonds
		Met A:10 - Ser A:11	[ RasMol ]
		Met B:10 - Ser B:11	[ RasMol ]
		Met C:10 - Ser C:11	[ RasMol ]
		Met D:10 - Ser D:11	[ RasMol ]

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

Still Images

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)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	5elm
		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
	C3SWD2_ECOLX \| C3SWD2
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	5.1.1.13
		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

Analysis Tools

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
	C3SWD2_ECOLX \| C3SWD2
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description