1Y5E - 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)

Title :   CRYSTAL STRUCTURE OF MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN B

Authors :   C. Chang, M. Zhou, J. Abdullah, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)

Date :   02 Dec 04 (Deposition) - 18 Jan 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Structural Genomics, Protein Structure Initiative, Psi, Mcsg, Midwest Center For Structural Genomics, Molybdenum Cofactor Biosynthesis, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Chang, M. Zhou, J. Abdullah, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Crystal Structure Of Molybdenum Cofactor Biosynthesis Protein B
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN B
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector	:	PLASMID
	Gene	:	MOAB
	Organism Scientific	:	BACILLUS CEREUS
	Organism Taxid	:	1396

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 14)

No.	Name	Count	Type	Full Name
1	IMD	1	Ligand/Ion	IMIDAZOLE
2	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (3, 14)

No.	Name	Count	Type	Full Name
1	IMD	1	Ligand/Ion	IMIDAZOLE
2	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (3, 28)

No.	Name	Count	Type	Full Name
1	IMD	2	Ligand/Ion	IMIDAZOLE
2	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	MSE	24	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER C:113 , ASP C:117 , GLY C:145 , ALA C:146 , HOH C:536	BINDING SITE FOR RESIDUE IMD C 501
2	AC2	SOFTWARE	ASP A:117 , SER A:143 , GLY A:145 , HOH A:276 , GLY B:145 , HOH B:519 , HOH B:525 , HOH B:612	BINDING SITE FOR RESIDUE MPD B 502

(no "SS Bond" information available for 1Y5E)

(no "Cis Peptide Bond" information available for 1Y5E)

(no "SAP(SNP)/Variant" information available for 1Y5E)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MOCF_BIOSYNTHESIS_1	PS01078	Molybdenum cofactor biosynthesis proteins signature 1.	MOAB_BACCR	75-88	3	A:75-88 B:75-88 C:75-88

Biological Unit 1 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MOCF_BIOSYNTHESIS_1	PS01078	Molybdenum cofactor biosynthesis proteins signature 1.	MOAB_BACCR	75-88	3	A:75-88 B:75-88 C:75-88

Biological Unit 2 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MOCF_BIOSYNTHESIS_1	PS01078	Molybdenum cofactor biosynthesis proteins signature 1.	MOAB_BACCR	75-88	6	A:75-88 B:75-88 C:75-88

(no "Exon" information available for 1Y5E)

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:157
 aligned with MOAB_BACCR | Q816R0 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:157
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       
           MOAB_BACCR    12 KEVRCKIVTISDTRTEETDKSGQLLHELLKEAGHKVTSYEIVKDDKESIQQAVLAGYHKEDVDVVLTNGGTGITKRDVTIEAVSALLDKEIVGFGELFRMISYLEDIGSSAMLSRAIGGTIGRKVVFSMPGSSGAVRLAMNKLILPELGHITFELHR 168
               SCOP domains d1y5ea1 A:12-166 MoaB                                                                                                                                      -- SCOP domains
               CATH domains 1y5eA00 A:12-168 Molybdenum Cofactor Biosythetic Enzyme; Chain A                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee........hhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhhh.....eeeee.........hhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhhhhh..eeeee..eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------MOCF_BIOSYNTHE-------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y5e A  12 KEVRCKIVTISDTRTEETDKSGQLLHELLKEAGHKVTSYEIVKDDKESIQQAVLAGYHKEDVDVVLTNGGTGITKRDVTIEAVSALLDKEIVGFGELFRmISYLEDIGSSAmLSRAIGGTIGRKVVFSmPGSSGAVRLAmNKLILPELGHITFELHR 168
                                    21        31        41        51        61        71        81        91       101       111       121 |     131       141       151       161       
                                                                                                                             111-MSE     123-MSE          140-MSE    151-MSE

Chain B from PDB  Type:PROTEIN  Length:160
 aligned with MOAB_BACCR | Q816R0 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:160
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168
           MOAB_BACCR     9 QAPKEVRCKIVTISDTRTEETDKSGQLLHELLKEAGHKVTSYEIVKDDKESIQQAVLAGYHKEDVDVVLTNGGTGITKRDVTIEAVSALLDKEIVGFGELFRMISYLEDIGSSAMLSRAIGGTIGRKVVFSMPGSSGAVRLAMNKLILPELGHITFELHR 168
               SCOP domains d1y5eb_ B: MoaB                                                                                                                                                  SCOP domains
               CATH domains 1y5eB00 B:9-168 Molybdenum Cofactor Biosythetic Enzyme; Chain A                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee........hhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhh....eeeee.........hhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhhhhh..eeeee..eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------MOCF_BIOSYNTHE-------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y5e B   9 QAPKEVRCKIVTISDTRTEETDKSGQLLHELLKEAGHKVTSYEIVKDDKESIQQAVLAGYHKEDVDVVLTNGGTGITKRDVTIEAVSALLDKEIVGFGELFRmISYLEDIGSSAmLSRAIGGTIGRKVVFSmPGSSGAVRLAmNKLILPELGHITFELHR 168
                                    18        28        38        48        58        68        78        88        98       108  |    118    |  128       138 |     148  |    158       168
                                                                                                                                111-MSE     123-MSE          140-MSE    151-MSE

Chain C from PDB  Type:PROTEIN  Length:161
 aligned with MOAB_BACCR | Q816R0 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:161
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168 
           MOAB_BACCR     9 QAPKEVRCKIVTISDTRTEETDKSGQLLHELLKEAGHKVTSYEIVKDDKESIQQAVLAGYHKEDVDVVLTNGGTGITKRDVTIEAVSALLDKEIVGFGELFRMISYLEDIGSSAMLSRAIGGTIGRKVVFSMPGSSGAVRLAMNKLILPELGHITFELHRQ 169
               SCOP domains d1y5ec_ C: MoaB                                                                                                                                                   SCOP domains
               CATH domains 1y5eC00 C:9-169 Molybdenum Cofactor Biosythetic Enzyme; Chain A                                                                                                   CATH domains
           Pfam domains (1) --------MoCF_biosynth-1y5eC01 C:17-161                                                                                                                   -------- Pfam domains (1)
           Pfam domains (2) --------MoCF_biosynth-1y5eC02 C:17-161                                                                                                                   -------- Pfam domains (2)
           Pfam domains (3) --------MoCF_biosynth-1y5eC03 C:17-161                                                                                                                   -------- Pfam domains (3)
         Sec.struct. author ......eeeeeee........hhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhh....eeeee.........hhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhhhhh..eeeee..eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------MOCF_BIOSYNTHE--------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y5e C   9 QAPKEVRCKIVTISDTRTEETDKSGQLLHELLKEAGHKVTSYEIVKDDKESIQQAVLAGYHKEDVDVVLTNGGTGITKRDVTIEAVSALLDKEIVGFGELFRmISYLEDIGSSAmLSRAIGGTIGRKVVFSmPGSSGAVRLAmNKLILPELGHITFELHRQ 169
                                    18        28        38        48        58        68        78        88        98       108  |    118    |  128       138 |     148  |    158       168 
                                                                                                                                111-MSE     123-MSE          140-MSE    151-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: Molybdenum cofactor biosynthesis proteins (49)

Superfamily: Molybdenum cofactor biosynthesis proteins (49)

Family: MogA-like (20)

Protein domain: MoaB (3)

Bacillus cereus [TaxId: 1396] (1)

1a	d1y5ea1	A:12-166
1b	d1y5eb_	B:
1c	d1y5ec_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Molybdenum Cofactor Biosythetic Enzyme; Chain A (34)

Homologous Superfamily: Molybdenum Cofactor Biosythetic Enzyme; Chain A (34)

Bacillus cereus. Organism_taxid: 1396. (1)

1a	1y5eC00	C:9-169
1b	1y5eB00	B:9-168
1c	1y5eA00	A:12-168

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: MoCF_biosynth] (31)

Family: MoCF_biosynth (31)

Bacillus cereus (strain ATCC 14579 / DSM 31) (1)

1a	MoCF_biosynth-1y5eC01	C:17-161
1b	MoCF_biosynth-1y5eC02	C:17-161
1c	MoCF_biosynth-1y5eC03	C:17-161

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (MOAB_BACCR | Q816R0)

molecular function
	GO:0061598	molybdopterin adenylyltransferase activity	Catalysis of the reaction ATP + molybdopterin = diphosphate + adenylyl-molybdopterin.
	GO:0061599	molybdopterin molybdotransferase activity	Catalysis of the reaction adenylyl-molybdopterin + molybdate = molybdenum cofactor + AMP.
biological process
	GO:0006777	Mo-molybdopterin cofactor biosynthetic process	The chemical reactions and pathways resulting in the formation of the Mo-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofactor consists of a mononuclear molybdenum (Mo) ion coordinated by one or two molybdopterin ligands.
	GO:0018315	molybdenum incorporation into molybdenum-molybdopterin complex	The incorporation of molybdenum into a molybdenum-molybdopterin complex.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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
		IMD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MPD	[ 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 1y5e)

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
	1y5e
		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
	MOAB_BACCR \| Q816R0
		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
	MOAB_BACCR \| Q816R0
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1Y5E)

(no "Related Entries Specified in the PDB File" available for 1Y5E)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 14)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (1, 3)

Pfam Domains (1, 3)

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