2W5U - JenaLib

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Title :   FLAVODOXIN FROM HELICOBACTER PYLORI IN COMPLEX WITH THE C3 INHIBITOR

Authors :   N. Cremades, I. Perez-Dorado, J. A. Hermoso, M. Martinez-Julvez, J. Sa

Date :   12 Dec 08 (Deposition) - 22 Dec 09 (Release) - 05 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.62

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

Keywords :   Drug Discovery, Electron Transport, Protein Hinhibitor, Fmn, Transport, Flavodoxin, Flavoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Cremades, A. Velazquez-Campoy, M. Martinez-Julvez, J. L. Neira, I. Perez-Dorado, J. Hermoso, P. Jimenez, A. Lanas, P. S. Hoffman, J. Sancho
Discovery Of Specific Flavodoxin Inhibitors As Potential Therapeutic Agents Against Helicobacter Pylori Infection.
Acs Chem. Biol. V. 4 928 2009
PubMed-ID: 19725577 | Reference-DOI: 10.1021/CB900166Q
(for further references see the PDB file header)

Molecule 1 - FLAVODOXIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A-FLDA
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	210

		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 (2, 3)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	IC3	1	Ligand/Ion	[2-(5-AMINO-4-CYANO-1H-PYRAZOL-1-YL)-5-(TRIFLUOROMETHYL)PHENYL](HYDROXY)OXOAMMONIUM

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	IC3	1	Ligand/Ion	[2-(5-AMINO-4-CYANO-1H-PYRAZOL-1-YL)-5-(TRIFLUOROMETHYL)PHENYL](HYDROXY)OXOAMMONIUM

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	IC3	-1	Ligand/Ion	[2-(5-AMINO-4-CYANO-1H-PYRAZOL-1-YL)-5-(TRIFLUOROMETHYL)PHENYL](HYDROXY)OXOAMMONIUM

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR B:10 , ASP B:11 , SER B:12 , GLY B:13 , ASN B:14 , ALA B:15 , PRO B:53 , THR B:54 , ALA B:55 , GLY B:56 , GLY B:58 , LEU B:86 , GLY B:87 , ASP B:88 , TYR B:92 , THR B:95 , PHE B:96 , ALA B:97 , ASP B:142 , HOH B:2012	BINDING SITE FOR RESIDUE FMN B 165
2	AC2	SOFTWARE	THR A:10 , ASP A:11 , SER A:12 , GLY A:13 , ASN A:14 , ALA A:15 , PRO A:53 , THR A:54 , ALA A:55 , GLY A:56 , ALA A:57 , GLY A:58 , LEU A:86 , GLY A:87 , ASP A:88 , TYR A:92 , THR A:95 , PHE A:96 , ALA A:97 , ASP A:142 , ALA A:164 , HOH A:2048	BINDING SITE FOR CHAIN A OF RESIDUES 165 TO 166

(no "SS Bond" information available for 2W5U)

(no "Cis Peptide Bond" information available for 2W5U)

(no "SAP(SNP)/Variant" information available for 2W5U)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FLAVODOXIN_LIKE	PS50902	Flavodoxin-like domain profile.	FLAV_HELPY	4-160	2	A:4-159 B:4-159

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FLAVODOXIN_LIKE	PS50902	Flavodoxin-like domain profile.	FLAV_HELPY	4-160	1	A:4-159 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FLAVODOXIN_LIKE	PS50902	Flavodoxin-like domain profile.	FLAV_HELPY	4-160	1	- B:4-159

(no "Exon" information available for 2W5U)

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:163
 aligned with FLAV_HELPY | O25776 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:163
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161   
           FLAV_HELPY     2 GKIGIFFGTDSGNAEAIAEKISKAIGNAEVVDVAKASKEQFNSFTKVILVAPTAGAGDLQTDWEDFLGTLEASDFATKTIGLVGLGDQDTYSETFAEGIFHIYEKAKAGKVVGQTPTDGYHFEASKAVEGGKFVGLVIDEDNQDDLTDERISKWVEQVKGSFA 164
               SCOP domains d2w5ua_ A: automated matches                                                                                                                                        SCOP domains
               CATH domains 2w5uA00 A:2-164  [code=3.40.50.360, no name defined]                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhhh.eeeee.hhhhhhhhh...eeeeee.eehhheehhhhhhhhhh.hhhhhh..eeeeeee...........hhhhhhhhhhh..eee...............ee..ee..eeehhhhhh.hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --FLAVODOXIN_LIKE  PDB: A:4-159 UniProt: 4-160                                                                                                                 ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w5u A   2 GKIGIFFGTDSGNAEAIAEKISKAIGNAEVVDVAKASKEQFNSFTKVILVAPTAGAGDLQTDWEDFLGTLEASDFANKTIGLVGLGDQDTYSETFAEGIFHIYEKAKAGKVVGQTSTDGYHFEASKAVEGGKFVGLVIDEDNQDDLTDERISKWVEQVRGSFA 164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain B from PDB  Type:PROTEIN  Length:163
 aligned with FLAV_HELPY | O25776 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:163
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161   
           FLAV_HELPY     2 GKIGIFFGTDSGNAEAIAEKISKAIGNAEVVDVAKASKEQFNSFTKVILVAPTAGAGDLQTDWEDFLGTLEASDFATKTIGLVGLGDQDTYSETFAEGIFHIYEKAKAGKVVGQTPTDGYHFEASKAVEGGKFVGLVIDEDNQDDLTDERISKWVEQVKGSFA 164
               SCOP domains d2w5ub_ B: automated matches                                                                                                                                        SCOP domains
               CATH domains 2w5uB00 B:2-164  [code=3.40.50.360, no name defined]                                                                                                                CATH domains
           Pfam domains (1) ----Flavodoxin_1-2w5uB01 B:6-155                                                                                                                          --------- Pfam domains (1)
           Pfam domains (2) ----Flavodoxin_1-2w5uB02 B:6-155                                                                                                                          --------- Pfam domains (2)
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhhh.eeeee....hhhhhh...eeeeee.eehhheehhhhhhhhhh..hhhhhh.eeeeeee............hhhhhhhhhh..ee................ee..ee..eee....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --FLAVODOXIN_LIKE  PDB: B:4-159 UniProt: 4-160                                                                                                                 ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w5u B   2 GKIGIFFGTDSGNAEAIAEKISKAIGNAEVVDVAKASKEQFNSFTKVILVAPTAGAGDLQTDWEDFLGTLEASDFANKTIGLVGLGDQDTYSETFAEGIFHIYEKAKAGKVVGQTSTDGYHFEASKAVEGGKFVGLVIDEDNQDDLTDERISKWVEQVRGSFA 164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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: Flavodoxin-like (1057)

Superfamily: Flavoproteins (208)

Family: Flavodoxin-related (81)

Protein domain: automated matches (9)

Helicobacter pylori [TaxId: 210] (2)

1a	d2w5ua_	A:
1b	d2w5ub_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.360, no name defined] (150)

Helicobacter pylori. Organism_taxid: 210. (3)

1a	2w5uA00	A:2-164
1b	2w5uB00	B:2-164

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Flavoprotein (71)

Family: Flavodoxin_1 (23)

Helicobacter pylori (Campylobacter pylori) (1)

1a	Flavodoxin_1-2w5uB01	B:6-155
1b	Flavodoxin_1-2w5uB02	B:6-155

Asymmetric Unit(hide GO term definitions)

Chain A,B (FLAV_HELPY | O25776)

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.
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.

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	FLAV_HELPY \| O25776	:	2bmv

2bmv	APOFLAVODOXIN FROM HELICOBACTER PYLORI

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