1S96 - JenaLib

Asym.Unit - manually (Jmol Viewer)

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)

Title :   THE 2.0 A X-RAY STRUCTURE OF GUANYLATE KINASE FROM E.COLI

Authors :   A. Kreusch, G. Spraggon, H. E. Klock, D. Mcmullan, J. Vincent, K. Rodrigues, S. A. Lesley

Date :   03 Feb 04 (Deposition) - 10 Feb 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   X-Ray Structure, Guanylate Kinase, E. Coli, Dimer, Sad, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Kreusch, G. Spraggon, H. E. Klock, D. Mcmullan, J. Vincent, K. Rodrigues, S. A. Lesley
The Structure Of Guanylate Kinase From Escherichia Coli At 2. 0 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - GUANYLATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.4.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	MH4
	Expression System Strain	:	DL41
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GMK, SPOR, B3648, C4473, SF3688, S4081
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	GMP KINASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 13)

No.	Name	Count	Type	Full Name
1	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
2	PO4	2	Ligand/Ion	PHOSPHATE ION
3	UNX	1	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 1 (3, 13)

No.	Name	Count	Type	Full Name
1	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
2	PO4	2	Ligand/Ion	PHOSPHATE ION
3	UNX	1	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 2 (3, 39)

No.	Name	Count	Type	Full Name
1	MSE	30	Mod. Amino Acid	SELENOMETHIONINE
2	PO4	6	Ligand/Ion	PHOSPHATE ION
3	UNX	3	Ligand/Ion	UNKNOWN ATOM OR ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:13 , GLY A:14 , ALA A:15 , GLY A:16 , UNX A:402 , HOH A:482	BINDING SITE FOR RESIDUE PO4 A 401
2	AC2	SOFTWARE	GLY B:14 , ALA B:15 , GLY B:16 , HOH B:633	BINDING SITE FOR RESIDUE PO4 B 501
3	AC3	SOFTWARE	SER A:18 , PO4 A:401 , HOH A:482 , HOH A:514	BINDING SITE FOR RESIDUE UNX A 402

(no "SS Bond" information available for 1S96)

(no "Cis Peptide Bond" information available for 1S96)

(no "SAP(SNP)/Variant" information available for 1S96)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GUANYLATE_KINASE_2	PS50052	Guanylate kinase-like domain profile.	KGUA_ECOLI	4-184	2	A:4-184 B:4-184
2	GUANYLATE_KINASE_1	PS00856	Guanylate kinase-like signature.	KGUA_ECOLI	40-57	2	A:40-57 B:40-57

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GUANYLATE_KINASE_2	PS50052	Guanylate kinase-like domain profile.	KGUA_ECOLI	4-184	2	A:4-184 B:4-184
2	GUANYLATE_KINASE_1	PS00856	Guanylate kinase-like signature.	KGUA_ECOLI	40-57	2	A:40-57 B:40-57

Biological Unit 2 (2, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GUANYLATE_KINASE_2	PS50052	Guanylate kinase-like domain profile.	KGUA_ECOLI	4-184	6	A:4-184 B:4-184
2	GUANYLATE_KINASE_1	PS00856	Guanylate kinase-like signature.	KGUA_ECOLI	40-57	6	A:40-57 B:40-57

(no "Exon" information available for 1S96)

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:205
 aligned with KGUA_ECOLI | P60546 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:205
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202     
           KGUA_ECOLI     3 QGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEVHGEHYFFVNHDEFKEMISRDAFLEHAEVFGNYYGTSREAIEQVLATGVDVFLDIDWQGAQQIRQKMPHARSIFILPPSKIELDRRLRGRGQDSEEVIAKRMAQAVAEMSHYAEYDYLIVNDDFDTALTDLKTIIRAERLRMSRQKQRHDALISKLLAD 207
               SCOP domains d1s96a_ A: Guanylate kinase                                                                                                                                                                                   SCOP domains
               CATH domains 1s96A01 A:3-36,A:97-207           1s96A02 A:37-96 Guanylate Kinase phosphate binding domain   1s96A01 A:3-36,A:97-207 P-loop containing nucleotide triphosphate hydrolases                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhh....eee...ee..............ee.hhhhhhhhhhh..eeeeeee..eeeeeehhhhhhhhh...eeeee.hhhhhhhhhhhh...eeeeee..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -GUANYLATE_KINASE_2  PDB: A:4-184 UniProt: 4-184                                                                                                                                      ----------------------- PROSITE (1)
                PROSITE (2) -------------------------------------GUANYLATE_KINASE_1------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s96 A   3 QGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEVHGEHYFFVNHDEFKEmISRDAFLEHAEVFGNYYGTSREAIEQVLATGVDVFLDIDWQGAQQIRQKmPHARSIFILPPSKIELDRRLRGRGQDSEEVIAKRmAQAVAEmSHYAEYDYLIVNDDFDTALTDLKTIIRAERLRmSRQKQRHDALISKLLAD 207
                                    12        22        32        42        52        62  |     72        82        92       102       112  |    122       132       142       152    |  162       172       182       192       202     
                                                                                         65-MSE                                           115-MSE                            150-MSE  |                              190-MSE             
                                                                                                                                                                                    157-MSE

Chain B from PDB  Type:PROTEIN  Length:204
 aligned with KGUA_ECOLI | P60546 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:204
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202    
           KGUA_ECOLI     3 QGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEVHGEHYFFVNHDEFKEMISRDAFLEHAEVFGNYYGTSREAIEQVLATGVDVFLDIDWQGAQQIRQKMPHARSIFILPPSKIELDRRLRGRGQDSEEVIAKRMAQAVAEMSHYAEYDYLIVNDDFDTALTDLKTIIRAERLRMSRQKQRHDALISKLLA 206
               SCOP domains d1s96b_ B: Guanylate kinase                                                                                                                                                                                  SCOP domains
               CATH domains 1s96B01 B:3-36,B:97-206           1s96B02 B:37-96 Guanylate Kinase phosphate binding domain   1s96B01 B:3-36,B:97-206 P-loop containing nucleotide triphosphate hydrolases                                   CATH domains
           Pfam domains (1) Guanylate_kin-1s96B01 B:3-186                                                                                                                                                           -------------------- Pfam domains (1)
           Pfam domains (2) Guanylate_kin-1s96B02 B:3-186                                                                                                                                                           -------------------- Pfam domains (2)
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhh....eee...ee..............ee.hhhhhhhhhhh..eeeeee....eeeeehhhhhhhhh...eeeee.hhhhhhhhhhhh...eeeeee..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -GUANYLATE_KINASE_2  PDB: B:4-184 UniProt: 4-184                                                                                                                                      ---------------------- PROSITE (1)
                PROSITE (2) -------------------------------------GUANYLATE_KINASE_1----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1s96 B   3 QGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEVHGEHYFFVNHDEFKEmISRDAFLEHAEVFGNYYGTSREAIEQVLATGVDVFLDIDWQGAQQIRQKmPHARSIFILPPSKIELDRRLRGRGQDSEEVIAKRmAQAVAEmSHYAEYDYLIVNDDFDTALTDLKTIIRAERLRmSRQKQRHDALISKLLA 206
                                    12        22        32        42        52        62  |     72        82        92       102       112  |    122       132       142       152    |  162       172       182       192       202    
                                                                                         65-MSE                                           115-MSE                            150-MSE  |                              190-MSE            
                                                                                                                                                                                    157-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: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: Nucleotide and nucleoside kinases (231)

Protein domain: Guanylate kinase (13)

Escherichia coli [TaxId: 562] (6)

1a	d1s96a_	A:
1b	d1s96b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Guanylate Kinase phosphate binding domain (22)

Homologous Superfamily: Guanylate Kinase phosphate binding domain (22)

Escherichia coli. Organism_taxid: 562. (4)

1a	1s96A02	A:37-96
1b	1s96B02	B:37-96

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

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Escherichia coli. Organism_taxid: 562. (54)

2a	1s96A01	A:3-36,A:97-207
2b	1s96B01	B:3-36,B:97-206

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Guanylate_kin (23)

Escherichia coli (strain K12) (1)

1a	Guanylate_kin-1s96B01	B:3-186
1b	Guanylate_kin-1s96B02	B:3-186

Asymmetric Unit(hide GO term definitions)

Chain A,B (KGUA_ECOLI | P60546)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004385	guanylate kinase activity	Catalysis of the reaction: ATP + GMP = ADP + GDP.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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.
	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.
biological process
	GO:0046710	GDP metabolic process	The chemical reactions and pathways involving GDP, guanosine 5'-diphosphate.
	GO:0046037	GMP metabolic process	The chemical reactions and pathways involving GMP, guanosine monophosphate.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0006163	purine nucleotide metabolic process	The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
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.

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
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		UNX	[ 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 1s96)

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 \| 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)

Access by PDB/NDB ID
	1s96
		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
	KGUA_ECOLI \| P60546
		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)
	2.7.4.8
		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
	KGUA_ECOLI \| P60546
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	KGUA_ECOLI \| P60546	:	2an9 2anb 2anc 2f3r 2f3t

(no "Related Entries Specified in the PDB File" available for 1S96)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 13)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (2, 4)

Pfam Domains (1, 2)

Gene Ontology (12, 12)

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