2Q1W - 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 THE BORDETELLA BRONCHISEPTICA ENZYME WBMH IN COMPLEX WITH NAD+

Authors :   J. D. King, N. J. Harmer, D. J. Maskell, T. L. Blundell

Date :   25 May 07 (Deposition) - 02 Oct 07 (Release) - 12 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.19

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

Keywords :   Rossmann Fold, Protein-Nad Complex, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. D. King, N. J. Harmer, A. Preston, C. M. Palmer, M. Rejzek, R. A. Field T. L. Blundell, D. J. Maskell
Predicting Protein Function From Structure--The Roles Of Short-Chain Dehydrogenase/Reductase Enzymes In Bordetella O-Antigen Biosynthesis.
J. Mol. Biol. V. 374 749 2007
PubMed-ID: 17950751 | Reference-DOI: 10.1016/J.JMB.2007.09.055
(for further references see the PDB file header)

Molecule 1 - PUTATIVE NUCLEOTIDE SUGAR EPIMERASE/ DEHYDRATASE
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	BBLPS1.14, WBMH
	Organism Scientific	:	BORDETELLA BRONCHISEPTICA
	Organism Taxid	:	518

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	NAD	3	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:8 , CYS A:10 , GLY A:11 , GLN A:12 , ILE A:13 , ASP A:32 , ASN A:33 , PHE A:34 , ALA A:35 , THR A:36 , GLY A:37 , GLY A:53 , SER A:54 , ILE A:55 , THR A:76 , ALA A:77 , ALA A:78 , TYR A:80 , THR A:92 , PHE A:115 , TYR A:143 , LYS A:147 , ASN A:168 , VAL A:169 , HOH A:505 , HOH A:510 , HOH A:528 , HOH A:544	BINDING SITE FOR RESIDUE NAD A 501
2	AC2	SOFTWARE	GLY B:8 , CYS B:10 , GLY B:11 , GLN B:12 , ILE B:13 , ASP B:32 , ASN B:33 , PHE B:34 , ALA B:35 , THR B:36 , GLY B:37 , GLY B:53 , SER B:54 , ILE B:55 , THR B:76 , ALA B:77 , ALA B:78 , TYR B:80 , THR B:92 , PHE B:115 , GLN B:116 , TYR B:143 , LYS B:147 , ALA B:167 , ASN B:168 , VAL B:169 , HOH B:503 , HOH B:504 , HOH B:548	BINDING SITE FOR RESIDUE NAD B 501
3	AC3	SOFTWARE	GLY C:8 , CYS C:10 , GLY C:11 , GLN C:12 , ILE C:13 , ASP C:32 , ASN C:33 , PHE C:34 , ALA C:35 , THR C:36 , GLY C:37 , GLY C:53 , SER C:54 , ILE C:55 , THR C:76 , ALA C:77 , ALA C:78 , TYR C:80 , THR C:92 , PHE C:115 , GLN C:116 , TYR C:143 , LYS C:147 , LEU C:166 , ASN C:168 , VAL C:169 , HOH C:507 , HOH C:513 , HOH C:516	BINDING SITE FOR RESIDUE NAD C 501

(no "SS Bond" information available for 2Q1W)

Asymmetric Unit

No.	Residues
1	Gln A:128	-	Pro A:129
2	Gln B:128	-	Pro B:129
3	Gln C:128	-	Pro C:129

(no "SAP(SNP)/Variant" information available for 2Q1W)

(no "PROSITE Motif" information available for 2Q1W)

(no "Exon" information available for 2Q1W)

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:300
 aligned with O87987_BORBO | O87987 from UniProtKB/TrEMBL  Length:313

    Alignment length:300
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300
         O87987_BORBO     1 MKKVFITGICGQIGSHIAELLLERGDKVVGIDNFATGRREHLKDHPNLTFVEGSIADHALVNQLIGDLQPDAVVHTAASYKDPDDWYNDTLTNCVGGSNVVQAAKKNNVGRFVYFQTALCYGVKPIQQPVRLDHPRNPANSSYAISKSANEDYLEYSGLDFVTFRLANVVGPRNVSGPLPIFFQRLSEGKKCFVTKARRDFVFVKDLARATVRAVDGVGHGAYHFSSGTDVAIKELYDAVVEAMALPSYPEPEIRELGPDDAPSILLDPSRTIQDFGKIEFTPLKETVAAAVAYFREYGV 300
               SCOP domains d2q1wa_ A: automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeee.....hhhhh.....eeeee....hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh..................hhhhhhhhhhhhhhhhhh..eeeeee.eee......hhhhhhhhhhhh....eeee.ee.eeehhhhhhhhhhhhh....eeee......eehhhhhhhhhhhh........eeee............hhhhhhhhh.....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2q1w A   1 MKKVFITGICGQIGSHIAELLLERGDKVVGIDNFATGRREHLKDHPNLTFVEGSIADHALVNQLIGDLQPDAVVHTAASYKDPDDWYNDTLTNCVGGSNVVQAAKKNNVGRFVYFQTALCYGVKPIQQPVRLDHPRNPANSSYAISKSANEDYLEYSGLDFVTFRLANVVGPRNVSGPLPIFFQRLSEGKKCFVTKARRDFVFVKDLARATVRAVDGVGHGAYHFSSGTDVAIKELYDAVVEAMALPSYPEPEIRELGPDDAPSILLDPSRTIQDFGKIEFTPLKETVAAAVAYFREYGV 300
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300

Chain B from PDB  Type:PROTEIN  Length:299
 aligned with O87987_BORBO | O87987 from UniProtKB/TrEMBL  Length:313

    Alignment length:301
                             1                                                                                                                                                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299 
         O87987_BORBO     - -MKKVFITGICGQIGSHIAELLLERGDKVVGIDNFATGRREHLKDHPNLTFVEGSIADHALVNQLIGDLQPDAVVHTAASYKDPDDWYNDTLTNCVGGSNVVQAAKKNNVGRFVYFQTALCYGVKPIQQPVRLDHPRNPANSSYAISKSANEDYLEYSGLDFVTFRLANVVGPRNVSGPLPIFFQRLSEGKKCFVTKARRDFVFVKDLARATVRAVDGVGHGAYHFSSGTDVAIKELYDAVVEAMALPSYPEPEIRELGPDDAPSILLDPSRTIQDFGKIEFTPLKETVAAAVAYFREYGV 300
               SCOP domains d2q1wb_ B: automated matches                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhh..eeeeee.....hhhhh.....eeeee....hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh..................hhhhhhhhhhhhhhhhhh..eeeeee.eee......hhhhhhhhhhhhh...eee..ee.eeehhhhhhhhhhhhh....eeee......eehhhhhhhhhhhhh.......eee..--.........hhhhhhhhh.....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q1w B   0 HMKKVFITGICGQIGSHIAELLLERGDKVVGIDNFATGRREHLKDHPNLTFVEGSIADHALVNQLIGDLQPDAVVHTAASYKDPDDWYNDTLTNCVGGSNVVQAAKKNNVGRFVYFQTALCYGVKPIQQPVRLDHPRNPANSSYAISKSANEDYLEYSGLDFVTFRLANVVGPRNVSGPLPIFFQRLSEGKKCFVTKARRDFVFVKDLARATVRAVDGVGHGAYHFSSGTDVAIKELYDAVVEAMALPSYPEPEIREL--DDAPSILLDPSRTIQDFGKIEFTPLKETVAAAVAYFREYGV 300
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       | -|      269       279       289       299 
                                                                                                                                                                                                                                                                                           257  |                                        
                                                                                                                                                                                                                                                                                              260

Chain C from PDB  Type:PROTEIN  Length:296
 aligned with O87987_BORBO | O87987 from UniProtKB/TrEMBL  Length:313

    Alignment length:300
                             1                                                                                                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299
         O87987_BORBO     - -MKKVFITGICGQIGSHIAELLLERGDKVVGIDNFATGRREHLKDHPNLTFVEGSIADHALVNQLIGDLQPDAVVHTAASYKDPDDWYNDTLTNCVGGSNVVQAAKKNNVGRFVYFQTALCYGVKPIQQPVRLDHPRNPANSSYAISKSANEDYLEYSGLDFVTFRLANVVGPRNVSGPLPIFFQRLSEGKKCFVTKARRDFVFVKDLARATVRAVDGVGHGAYHFSSGTDVAIKELYDAVVEAMALPSYPEPEIRELGPDDAPSILLDPSRTIQDFGKIEFTPLKETVAAAVAYFREYG 299
               SCOP domains d2q1wc_ C: automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhh..eeeeee.....hhhhh.....eeeee....hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh..................hhhhhhhhhhhhhhhhhh..eeeeee..ee....-.hhhhhhhhhhhh....eee..ee..eehhhhhhhhhhhhh....eeee......eehhhhhhhhhhhhh.......eee...---.......hhhhhhhhh.....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2q1w C   0 HMKKVFITGICGQIGSHIAELLLERGDKVVGIDNFATGRREHLKDHPNLTFVEGSIADHALVNQLIGDLQPDAVVHTAASYKDPDDWYNDTLTNCVGGSNVVQAAKKNNVGRFVYFQTALCYGVKPIQQPVRLDHPRNPANSSYAISKSANEDYLEYSGLDFVTFRLANVVGPRN-SGPLPIFFQRLSEGKKCFVTKARRDFVFVKDLARATVRAVDGVGHGAYHFSSGTDVAIKELYDAVVEAMALPSYPEPEIRELG---APSILLDPSRTIQDFGKIEFTPLKETVAAAVAYFREYG 299
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169    | |179       189       199       209       219       229       239       249        |-  |    269       279       289       299
                                                                                                                                                                                                        174 |                                                                               258 262                                     
                                                                                                                                                                                                          176

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: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: automated matches (447)

Protein domain: automated matches (447)

Bordetella bronchiseptica [TaxId: 518] (6)

1a	d2q1wa_	A:
1b	d2q1wb_	B:
1c	d2q1wc_	C:

(no "CATH Domain" information available for 2Q1W)

(no "Pfam Domain" information available for 2Q1W)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (O87987_BORBO | O87987)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0050662	coenzyme binding	Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
	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:0006541	glutamine metabolic process	The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.

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

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

	Cis Peptide Bonds
		Gln A:128 - Pro A:129	[ RasMol ]
		Gln B:128 - Pro B:129	[ RasMol ]
		Gln C:128 - Pro C:129	[ RasMol ]

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
	2q1w
		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
	O87987_BORBO \| O87987
		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
	O87987_BORBO \| O87987
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 2Q1W)

2pzk	CLOSEST KNOWN HOMOLOGUE, USED AS A SEARCH MODEL FOR MOLECULAR REPLACEMENT.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

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