2HKL - 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)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ENTEROCOCCUS FAECIUM L,D-TRANSPEPTIDASE C442S MUTANT

Authors :   V. Delfosse, J. -E. Hugonnet, S. Magnet, J. -L. Mainardi, M. Arthur, C. Mayer

Date :   05 Jul 06 (Deposition) - 22 May 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   L, D-Transpeptidase, Antibiotic Resistance, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Delfosse, J. -E. Hugonnet, S. Magnet, J. -L. Mainardi, M. Arthur, C. Mayer
Crystal Structure Of Enterococcus Faecium L, D-Transpeptidase C442S Mutant
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - L,D-TRANSPEPTIDASE
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET2818
	Expression System Strain	:	BL21-DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL RESIDUES 217-466
	Gene	:	LDTFM
	Mutation	:	YES
	Organism Scientific	:	ENTEROCOCCUS FAECIUM
	Organism Taxid	:	1352
	Strain	:	M512

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:393 , HIS A:421 , SER A:439 , HIS A:440 , ASN A:444	BINDING SITE FOR RESIDUE SO4 A 1
2	AC2	SOFTWARE	HIS B:421 , SER B:439 , HIS B:440 , ASN B:444	BINDING SITE FOR RESIDUE SO4 B 2
3	AC3	SOFTWARE	HIS C:421 , SER C:439 , HIS C:440 , SER C:442 , ASN C:444	BINDING SITE FOR RESIDUE SO4 C 3

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

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

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

(no "PROSITE Motif" information available for 2HKL)

(no "Exon" information available for 2HKL)

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:248
 aligned with Q3Y185_ENTFC | Q3Y185 from UniProtKB/TrEMBL  Length:466

    Alignment length:250
                                   226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466
         Q3Y185_ENTFC   217 KEQLASMNAIANVKATYSINGETFQIPSSDIMSWLTYNDGKVDLDTEQVRQYVTDLGTKYNTSTNDTKFKSTKRGEVTVPVGTYSWTIQTDSETEALKKAILAGQDFTRSPIVQGGTTADHPLIEDTYIEVDLENQHMWYYKDGKVALETDIVSGKPTTPTPAGVFYVWNKEEDATLKGTNDDGTPYESPVNYWMPIDWTGVGIHDSDWQPEYGGDLWKTRGSHGCINTPPSVMKELFGMVEKGTPVLVF 466
               SCOP domains d2hkla1 A:217-338 L,D-transpeptidase, pre-catalytic domain                                                                d2hkla2 A:339-466 L,D-transpeptidase, C-terminal, catalytic   domain                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..eeeee..eeee.hhhhhhhheeee..eeeehhhhhhhhhhhhhhhhh.....eeee.....eeee......eeehhhhhhhhhhhhhhh...eee...eee............eeeee....eeeeee..eeeeeee............eeee....eeeee..ee.--..ee..eeeeeee......eeee.........hhhhhhh....eeehhhhhhhhhhhh....eeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hkl A 217 KEQLASMNAIANVKATYSINGETFQIPSSDIMSWLTYNDGKVDLDTEQVRQYVTDLGTKYNTSTNDTKFKSTKRGEVTVPVGTYSWTIQTDSETEALKKAILAGQDFTRSPIVQGGTTADHPLIEDTYIEVDLENQHMWYYKDGKVALETDIVSGKPTTPTPAGVFYVWNKEEDATLKGTN--GTPYESPVNYWMPIDWTGVGIHDSDWQPEYGGDLWKTRGSHGSINTPPSVMKELFGMVEKGTPVLVF 466
                                   226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396|  |   406       416       426       436       446       456       466
                                                                                                                                                                                                              397  |                                                                  
                                                                                                                                                                                                                 400

Chain B from PDB  Type:PROTEIN  Length:248
 aligned with Q3Y185_ENTFC | Q3Y185 from UniProtKB/TrEMBL  Length:466

    Alignment length:250
                                   226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466
         Q3Y185_ENTFC   217 KEQLASMNAIANVKATYSINGETFQIPSSDIMSWLTYNDGKVDLDTEQVRQYVTDLGTKYNTSTNDTKFKSTKRGEVTVPVGTYSWTIQTDSETEALKKAILAGQDFTRSPIVQGGTTADHPLIEDTYIEVDLENQHMWYYKDGKVALETDIVSGKPTTPTPAGVFYVWNKEEDATLKGTNDDGTPYESPVNYWMPIDWTGVGIHDSDWQPEYGGDLWKTRGSHGCINTPPSVMKELFGMVEKGTPVLVF 466
               SCOP domains d2hklb1 B:217-338 L,D-transpeptidase, pre-catalytic domain                                                                d2hklb2 B:339-466 L,D-transpeptidase, C-terminal, catalytic   domain                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh..eeeee..eeee.hhhhhhhheeee..eeeehhhhhhhhhhhhhhhhh.....eeee.....eeee......eeehhhhhhhhhhhhhhh...eee...eee............eeeee....eeeeee..eeeeeee............eeee....eeeee..ee.--..ee..eeeeeee......eeee.........hhhhhhh....eeehhhhhhhhhhhh....eeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hkl B 217 KEQLASMNAIANVKATYSINGETFQIPSSDIMSWLTYNDGKVDLDTEQVRQYVTDLGTKYNTSTNDTKFKSTKRGEVTVPVGTYSWTIQTDSETEALKKAILAGQDFTRSPIVQGGTTADHPLIEDTYIEVDLENQHMWYYKDGKVALETDIVSGKPTTPTPAGVFYVWNKEEDATLKGTN--GTPYESPVNYWMPIDWTGVGIHDSDWQPEYGGDLWKTRGSHGSINTPPSVMKELFGMVEKGTPVLVF 466
                                   226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396|  |   406       416       426       436       446       456       466
                                                                                                                                                                                                              397  |                                                                  
                                                                                                                                                                                                                 400

Chain C from PDB  Type:PROTEIN  Length:248
 aligned with Q3Y185_ENTFC | Q3Y185 from UniProtKB/TrEMBL  Length:466

    Alignment length:250
                                   226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466
         Q3Y185_ENTFC   217 KEQLASMNAIANVKATYSINGETFQIPSSDIMSWLTYNDGKVDLDTEQVRQYVTDLGTKYNTSTNDTKFKSTKRGEVTVPVGTYSWTIQTDSETEALKKAILAGQDFTRSPIVQGGTTADHPLIEDTYIEVDLENQHMWYYKDGKVALETDIVSGKPTTPTPAGVFYVWNKEEDATLKGTNDDGTPYESPVNYWMPIDWTGVGIHDSDWQPEYGGDLWKTRGSHGCINTPPSVMKELFGMVEKGTPVLVF 466
               SCOP domains d2hklc1 C:217-338 L,D-transpeptidase, pre-catalytic domain                                                                d2hklc2 C:339-466 L,D-transpeptidase, C-terminal, catalytic   domain                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..eeeee..eeee.hhhhhhhheeee..eeeehhhhhhhhhhhhhhhhh.....eeee.....eeee......eeehhhhhhhhhhhhhhh...eee...eee............eeeee....eeeeee..eeeeeee............eeee....eeeeeeee..--...eeeeeeeeee......eeee.........hhhhhhh....eeehhhhhhhhhhhh....eeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hkl C 217 KEQLASMNAIANVKATYSINGETFQIPSSDIMSWLTYNDGKVDLDTEQVRQYVTDLGTKYNTSTNDTKFKSTKRGEVTVPVGTYSWTIQTDSETEALKKAILAGQDFTRSPIVQGGTTADHPLIEDTYIEVDLENQHMWYYKDGKVALETDIVSGKPTTPTPAGVFYVWNKEEDATLKGTN--GTPYESPVNYWMPIDWTGVGIHDSDWQPEYGGDLWKTRGSHGSINTPPSVMKELFGMVEKGTPVLVF 466
                                   226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396|  |   406       416       426       436       446       456       466
                                                                                                                                                                                                              397  |                                                                  
                                                                                                                                                                                                                 400

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 "CATH Domain" information available for 2HKL)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (Q3Y185_ENTFC | Q3Y185)

molecular function
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

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

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ 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 \| Biol. Unit 3 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
	2hkl
		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
	Q3Y185_ENTFC \| Q3Y185
		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)
	(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
	Q3Y185_ENTFC \| Q3Y185
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q3Y185_ENTFC \| Q3Y185	:	1zat 3zg4 3zgp

1zat	APOPROTEIN WILD TYPE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 6)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (3, 3)

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