3QVH - JenaLib

Title :   CRYSTAL STRUCTURE OF FOSFOMYCIN RESISTANCE KINASE FOMA FROM STREPTOMYCES WEDMORENSIS COMPLEXED WITH ADP

Authors :   S. Pakhomova, S. G. Bartlett, P. A. Doerner, M. E. Newcomer

Date :   25 Feb 11 (Deposition) - 20 Jul 11 (Release) - 29 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Fosfomycin, Antibiotic Resistance, Phosphoryl Transfer, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Pakhomova, S. G. Bartlett, P. A. Doerner, M. E. Newcomer
Structural And Biochemical Insights Into The Mechanism Of Fosfomycin Phosphorylation By Fosfomycin Resistance Kinase Foma.
Biochemistry V. 50 6909 2011
PubMed-ID: 21728358 | Reference-DOI: 10.1021/BI2004334

Compounds

Molecule 1 - FOMA PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	FOMA, FOSFOMYCIN RESISTANCE KINASE
	Organism Scientific	:	STREPTOMYCES WEDMORENSIS
	Organism Taxid	:	43759

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE

Sites (1, 1)

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:9 , GLY A:11 , GLY A:12 , SER A:13 , THR A:170 , ASP A:171 , VAL A:172 , GLY A:174 , ILE A:175 , VAL A:176 , ALA A:200 , LEU A:201 , SER A:204 , ALA A:212 , MET A:213 , LYS A:216 , HOH A:273 , HOH A:283 , HOH A:319 , HOH A:354 , HOH A:358 , HOH A:408	BINDING SITE FOR RESIDUE ADP A 1260

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

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:260
 aligned with Q56187_STRWE | Q56187 from UniProtKB/TrEMBL  Length:266

    Alignment length:271
                                     1                                                                                                                                                                                                                                                                     
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261 
         Q56187_STRWE     - ---------MTPDFLAIKVGGSLFSRKDEPGSLDDDAVTPFARNFARLAETYRGRMVLISGGGAFGHGAIRDHDSTHAFSLAGLTEATFEVKKRWAEKLRGIGVDAFPLQLAAMCTLRNGIPQLRSEVLRDVLDHGALPVLAGDALFDEHGKLWAFSSDRVPEVLLPMVEGRLRVVTLTDVDGIVTDGAGGDTILPEVDARSPEQAYAALWGSSEWDATGAMHTKLDALVTCARRGAECFIMRGDPGSDLEFLTAPFSSWPAHVRSTRITT 262
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee.hhhh.........hhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhh.-----hhhhhhhhhhhhhhhhhhhhhhhhhh...eee.hhhh.eeee..eeee..hhhhhhhhh..eeeee.eeee.....eeeehhhhhhhhh.......eeeeeee.....ee......ee..eee...hhhhhhhhhhh------hhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhh......eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qvh A  -8 SGLVPRGSHMTPDFLAIKVGGSLFSRKDEPGSLDDDAVTRFARNFARLAETYRGRMVLISGGGAFGHGAIR-----HAFSLAGLTEATFEVKKRWAEKLRGIGVDAFPLQLAAMCTLRNGIPQLRSEVLRDVLDHGALPVLAGDALFDEHGKLWAFSSDRVPEVLLPMVEGRLRVVTLTDVDGIVTDGAGGDTILPEVDARSPEQAYAALWGS------GAMHTKLDALVTCARRGAECFIMRGDPGSDLEFLTAPFSSWPAHVRSTRITT 262
                                     1        11        21        31        41        51        61|     | 71        81        91       101       111       121       131       141       151       161       171       181       191       201  |    211       221       231       241       251       261 
                                                                                                 62    68                                                                                                                                     204    211

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 (5, 5)

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

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

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

Biological Unit
	Complete Structure
		Biological Unit 1	[ 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 ](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
	3qvh
		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
	Q56187_STRWE \| Q56187
		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

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
	Q56187_STRWE \| Q56187
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

3d40	CRYSTAL STRUCTURE OF FOSFOMYCIN RESISTANCE KINASE FOMA FROM STREPTOMYCES WEDMORENSIS COMPLEXED WITH DIPHOSPHATE
3d41	CRYSTAL STRUCTURE OF FOSFOMYCIN RESISTANCE KINASE FOMA FROM STREPTOMYCES WEDMORENSIS COMPLEXED WITH MGAMPPNP AND FOSFOMYCIN
3qun	CRYSTAL STRUCTURE OF FOSFOMYCIN RESISTANCE KINASE FOMA FROM STREPTOMYCES WEDMORENSIS COMPLEXED WITH MGATP
3quo	CRYSTAL STRUCTURE OF FOSFOMYCIN RESISTANCE KINASE FOMA FROM STREPTOMYCES WEDMORENSIS COMPLEXED WITH ATP AND FOSFOMYCIN
3qur	CRYSTAL STRUCTURE OF FOSFOMYCIN RESISTANCE KINASE FOMA FROM STREPTOMYCES WEDMORENSIS COMPLEXED WITH MGADP AND FOSFOMYCIN VANADATE
3qvf	CRYSTAL STRUCTURE OF FOSFOMYCIN RESISTANCE KINASE FOMA FROM STREPTOMYCES WEDMORENSIS COMPLEXED WITH MGADP AND FOSFOMYCIN MONOPHOSPHATE

Description