4A3U - 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 :   X-STRUCTURE OF THE OLD YELLOW ENZYME HOMOLOGUE FROM ZYMOMONAS MOBILIS (NCR)

Authors :   H. W. Hoeffken

Date :   04 Oct 11 (Deposition) - 17 Oct 12 (Release) - 07 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Reich, H. W. Hoeffken, B. Rosche, B. M. Nestl, B. Hauer
Crystal Structure Determination And Mutagenesis Analysis Of The Ene Reductase Ncr.
Chembiochem V. 13 2400 2012
PubMed-ID: 23033175 | Reference-DOI: 10.1002/CBIC.201200404

Molecule 1 - NADH:FLAVIN OXIDOREDUCTASE/NADH OXIDASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ZYMOMONAS MOBILIS
	Organism Taxid	:	542
	Synonym	:	NCR

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 11)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
3	K	2	Ligand/Ion	POTASSIUM ION
4	NA	3	Ligand/Ion	SODIUM ION
5	NCA	2	Ligand/Ion	NICOTINAMIDE

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
3	K	-1	Ligand/Ion	POTASSIUM ION
4	NA	-1	Ligand/Ion	SODIUM ION
5	NCA	1	Ligand/Ion	NICOTINAMIDE

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
3	K	-1	Ligand/Ion	POTASSIUM ION
4	NA	-1	Ligand/Ion	SODIUM ION
5	NCA	1	Ligand/Ion	NICOTINAMIDE

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA B:22 , PRO B:23 , LEU B:24 , THR B:25 , ALA B:56 , GLN B:98 , HIS B:172 , ASN B:175 , ARG B:224 , ARG B:261 , PHE B:269 , ASN B:292 , GLN B:293 , ASP B:294 , PHE B:314 , GLY B:315 , ARG B:316 , TRP B:342 , TYR B:343 , NCA B:1359 , HOH B:2191 , HOH B:2193 , HOH B:2205	BINDING SITE FOR RESIDUE FMN B1357
02	AC2	SOFTWARE	ALA A:22 , PRO A:23 , LEU A:24 , THR A:25 , ALA A:56 , GLN A:98 , HIS A:172 , ASN A:175 , ARG A:224 , ARG A:261 , PHE A:269 , ASN A:292 , GLN A:293 , ASP A:294 , PHE A:314 , GLY A:315 , ARG A:316 , TRP A:342 , TYR A:343 , NCA A:1359 , HOH A:2248 , HOH A:2250 , HOH A:2289	BINDING SITE FOR RESIDUE FMN A1357
03	AC3	SOFTWARE	PRO B:23 , ILE B:53 , GLN B:170 , ARG B:224 , GLY B:259 , VAL B:290 , SER B:313	BINDING SITE FOR RESIDUE ACT B1358
04	AC4	SOFTWARE	ILE A:53 , GLN A:170 , ARG A:224 , GLY A:259 , SER A:313	BINDING SITE FOR RESIDUE ACT A1358
05	AC5	SOFTWARE	THR B:25 , TRP B:66 , HIS B:172 , ASN B:175 , TYR B:177 , TYR B:343 , FMN B:1357 , HOH B:2115	BINDING SITE FOR RESIDUE NCA B1359
06	AC6	SOFTWARE	THR A:25 , TRP A:66 , HIS A:172 , ASN A:175 , TYR A:177 , TYR A:343 , FMN A:1357	BINDING SITE FOR RESIDUE NCA A1359
07	AC7	SOFTWARE	HIS A:89 , GLY B:11 , GLU B:219	BINDING SITE FOR RESIDUE NA A1360
08	AC8	SOFTWARE	ARG B:140 , ALA B:141 , HOH B:2100	BINDING SITE FOR RESIDUE NA B1360
09	AC9	SOFTWARE	LYS A:331 , SER B:119 , ALA B:120 , HIS B:189	BINDING SITE FOR RESIDUE NA B1361
10	BC1	SOFTWARE	LEU A:126 , TYR A:136 , HOH A:2057 , HOH A:2144	BINDING SITE FOR RESIDUE K A1361
11	BC2	SOFTWARE	ALA B:47 , ALA B:49 , HOH B:2013 , HOH B:2015 , HOH B:2069	BINDING SITE FOR RESIDUE K B1362

(no "SS Bond" information available for 4A3U)

(no "Cis Peptide Bond" information available for 4A3U)

(no "SAP(SNP)/Variant" information available for 4A3U)

(no "PROSITE Motif" information available for 4A3U)

(no "Exon" information available for 4A3U)

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:355
 aligned with Q5NLA1_ZYMMO | Q5NLA1 from UniProtKB/TrEMBL  Length:358

    Alignment length:355
                                    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       271       281       291       301       311       321       331       341       351     
         Q5NLA1_ZYMMO     2 PSLFDPIRFGAFTAKNRIWMAPLTRGRATRDHVPTEIMAEYYAQRASAGLIISEATGISQEGLGWPYAPGIWSDAQVEAWLPITQAVHDAGGLIFAQLWHMGRMVPSNVSGMQPVAPSASQAPGLGHTYDGKKPYDVARALRLDEIPRLLDDYEKAARHALKAGFDGVQIHAANGYLIDEFIRDSTNHRHDEYGGAVENRIRLLKDVTERVIATIGKERTAVRLSPNGEIQGTVDSHPEQVFIPAAKMLSDLDIAFLGMREGAVDGTFGKTDQPKLSPEIRKVFKPPLVLNQDYTFETAQAALDSGVADAISFGRPFIGNPDLPRRFFEKAPLTKDVIETWYTQTPKGYTDYPLL 356
               SCOP domains d4a3ua_ A: automated matches                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eee...eee..............hhhhhhhhhhh.....eeeeeee...............hhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh...ee...ee...eee....eee..eeee.hhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee.............hhhhhhhhhhhhhhhh..eeeee...............hhhhhhhhh...eeee...hhhhhhhhhhhh...eeeehhhhhhh.hhhhhhhhh......hhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a3u A   2 PSLFDPIRFGAFTAKNRIWMAPLTRGRATRDHVPTEIMAEYYAQRASAGLIISEATGISQEGLGWPYAPGIWSDAQVEAWLPITQAVHDAGGLIFAQLWHMGRMVPSNVSGMQPVAPSASQAPGLGHTYDGKKPYDVARALRLDEIPRLLDDYEKAARHALKAGFDGVQIHAANGYLIDEFIRDSTNHRHDEYGGAVENRIRLLKDVTERVIATIGKERTAVRLSPNGEIQGTVDSHPEQVFIPAAKMLSDLDIAFLGMREGAVDGTFGKTDQPKLSPEIRKVFKPPLVLNQDYTFETAQAALDSGVADAISFGRPFIGNPDLPRRFFEKAPLTKDVIETWYTQTPKGYTDYPLL 356
                                    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       271       281       291       301       311       321       331       341       351

Chain B from PDB  Type:PROTEIN  Length:355
 aligned with Q5NLA1_ZYMMO | Q5NLA1 from UniProtKB/TrEMBL  Length:358

    Alignment length:355
                                    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       271       281       291       301       311       321       331       341       351     
         Q5NLA1_ZYMMO     2 PSLFDPIRFGAFTAKNRIWMAPLTRGRATRDHVPTEIMAEYYAQRASAGLIISEATGISQEGLGWPYAPGIWSDAQVEAWLPITQAVHDAGGLIFAQLWHMGRMVPSNVSGMQPVAPSASQAPGLGHTYDGKKPYDVARALRLDEIPRLLDDYEKAARHALKAGFDGVQIHAANGYLIDEFIRDSTNHRHDEYGGAVENRIRLLKDVTERVIATIGKERTAVRLSPNGEIQGTVDSHPEQVFIPAAKMLSDLDIAFLGMREGAVDGTFGKTDQPKLSPEIRKVFKPPLVLNQDYTFETAQAALDSGVADAISFGRPFIGNPDLPRRFFEKAPLTKDVIETWYTQTPKGYTDYPLL 356
               SCOP domains d4a3ub_ B: automated matches                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eee...eee...............hhhhhhhhhh.....eeeeeee...............hhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh...ee........ee......ee....ee.hhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee.............hhhhhhhhhhhhhhhh..eeeee...............hhhhhhhhh...eeee...hhhhhhhhhhhh...eeeehhhhhhh.hhhhhhhh.......hhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a3u B   2 PSLFDPIRFGAFTAKNRIWMAPLTRGRATRDHVPTEIMAEYYAQRASAGLIISEATGISQEGLGWPYAPGIWSDAQVEAWLPITQAVHDAGGLIFAQLWHMGRMVPSNVSGMQPVAPSASQAPGLGHTYDGKKPYDVARALRLDEIPRLLDDYEKAARHALKAGFDGVQIHAANGYLIDEFIRDSTNHRHDEYGGAVENRIRLLKDVTERVIATIGKERTAVRLSPNGEIQGTVDSHPEQVFIPAAKMLSDLDIAFLGMREGAVDGTFGKTDQPKLSPEIRKVFKPPLVLNQDYTFETAQAALDSGVADAISFGRPFIGNPDLPRRFFEKAPLTKDVIETWYTQTPKGYTDYPLL 356
                                    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       271       281       291       301       311       321       331       341       351

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: TIM beta/alpha-barrel (3956)

Superfamily: FMN-linked oxidoreductases (290)

Family: automated matches (48)

Protein domain: automated matches (48)

Zymomonas mobilis [TaxId: 542] (1)

1a	d4a3ua_	A:
1b	d4a3ub_	B:

(no "CATH Domain" information available for 4A3U)

(no "Pfam Domain" information available for 4A3U)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q5NLA1_ZYMMO | Q5NLA1)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	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: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:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FMN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		K	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NCA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4a3u)

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
	4a3u
		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
	Q5NLA1_ZYMMO \| Q5NLA1
		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
	Q5NLA1_ZYMMO \| Q5NLA1
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q5NLA1_ZYMMO \| Q5NLA1	:	4ot7

(no "Related Entries Specified in the PDB File" available for 4A3U)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 11)

Sites (11, 11)

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 (1, 2)

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