2CZ6 - JenaLib

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Title :   COMPLEX OF INACTIVE FE-TYPE NHASE WITH CYCLOHEXYL ISOCYANIDE

Authors :   M. Nojiri, Y. Kawano, K. Hashimoto, N. Kamiya, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   11 Jul 05 (Deposition) - 11 Jan 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Cysteine-Sulfinic Acid, Cysteine-Sulfenic Acid, Photo- Reactive, Nitrile, Hydration, Substrate Analogue, Complex, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Nojiri, Y. Kawano, K. Hashimoto, N. Kamiya
X-Ray Snap Shots Of Inhibitor Binding Process In Photo-Reactive Nitrile Hydratase
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - NITRILE HYDRATASE SUBUNIT ALPHA
	Chains	:	A
	EC Number	:	4.2.1.84
	Organism Scientific	:	RHODOCOCCUS ERYTHROPOLIS
	Organism Taxid	:	1833
	Strain	:	N771
	Synonym	:	NITRILASE, NHASE

Molecule 2 - NITRILE HYDRATASE SUBUNIT BETA
	Chains	:	B
	EC Number	:	4.2.1.84
	Organism Scientific	:	RHODOCOCCUS ERYTHROPOLIS
	Organism Taxid	:	1833
	Strain	:	N771
	Synonym	:	NITRILASE, NHASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 9)

No.	Name	Count	Type	Full Name
1	CSD	1	Mod. Amino Acid	3-SULFINOALANINE
2	CSO	1	Mod. Amino Acid	S-HYDROXYCYSTEINE
3	CYI	1	Mod. Residue	CYCLOHEXYL ISOCYANIDE
4	FE	1	Ligand/Ion	FE (III) ION
5	MG	4	Ligand/Ion	MAGNESIUM ION
6	NO	1	Ligand/Ion	NITRIC OXIDE

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	CSD	1	Mod. Amino Acid	3-SULFINOALANINE
2	CSO	1	Mod. Amino Acid	S-HYDROXYCYSTEINE
3	CYI	1	Mod. Residue	CYCLOHEXYL ISOCYANIDE
4	FE	-1	Ligand/Ion	FE (III) ION
5	MG	-1	Ligand/Ion	MAGNESIUM ION
6	NO	-1	Ligand/Ion	NITRIC OXIDE

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	CSD	2	Mod. Amino Acid	3-SULFINOALANINE
2	CSO	2	Mod. Amino Acid	S-HYDROXYCYSTEINE
3	CYI	2	Mod. Residue	CYCLOHEXYL ISOCYANIDE
4	FE	-1	Ligand/Ion	FE (III) ION
5	MG	-1	Ligand/Ion	MAGNESIUM ION
6	NO	-1	Ligand/Ion	NITRIC OXIDE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:109 , CSD A:112 , SER A:113 , CSO A:114 , NO A:301	BINDING SITE FOR RESIDUE FE A 300
2	AC2	SOFTWARE	HOH B:1322 , HOH B:1363 , HOH B:1409 , HOH B:1412 , HOH B:1414 , HOH B:1449	BINDING SITE FOR RESIDUE MG B 1303
3	AC3	SOFTWARE	HOH A:1335 , HOH A:1494 , HOH A:1501 , HOH A:1519 , HOH B:1419 , HOH B:1532	BINDING SITE FOR RESIDUE MG A 1304
4	AC4	SOFTWARE	HOH A:1527 , HOH A:1604 , HOH A:1660 , HOH A:1665 , HOH B:1546	BINDING SITE FOR RESIDUE MG A 1305
5	AC5	SOFTWARE	HOH A:1472 , HOH A:1569 , HOH B:1561	BINDING SITE FOR RESIDUE MG A 1306
6	AC6	SOFTWARE	CSD A:112 , SER A:113 , CSO A:114 , FE A:300 , CYI B:1302	BINDING SITE FOR RESIDUE NO A 301
7	AC7	SOFTWARE	TRP A:117 , NO A:301 , HOH A:1373 , TYR B:37 , MET B:40 , ARG B:56 , TYR B:76	BINDING SITE FOR RESIDUE CYI B 1302

(no "SS Bond" information available for 2CZ6)

(no "Cis Peptide Bond" information available for 2CZ6)

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_NHAB_RHOER_001 *	M	40	V	NHAB_RHOER	---	---	B	M	40	V
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_NHAB_RHOER_001 *	M	40	V	NHAB_RHOER	---	---	B	M	40	V
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_NHAB_RHOER_001 *	M	40	V	NHAB_RHOER	---	---	B	M	40	V
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2CZ6)

(no "Exon" information available for 2CZ6)

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:197
 aligned with NHAA_RHOER | P13448 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:197
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       
           NHAA_RHOER    10 ENAAPAQAPVSDRAWALFRALDGKGLVPDGYVEGWKKTFEEDFSPRRGAELVARAWTDPEFRQLLLTDGTAAVAQYGYLGPQGEYIVAVEDTPTLKNVIVCSLCSCTAWPILGLPPTWYKSFEYRARVVREPRKVLSEMGTEIASDIEIRVYDTTAETRYMVLPQRPAGTEGWSQEQLQEIVTKDCLIGVAIPQVPT 206
               SCOP domains d2cz6a_ A: automated matches                                                                                                                                                                          SCOP domains
               CATH domains 2cz6A00 A:9-205 Nitrile Hydratase; Chain A                                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeee....eeeeee.......hhhhhh..hhhhhhhhhhhhh..hhhhhhhhhh.......eeeeee.....eeeee..........hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cz6 A   9 ENAAPAQAPVSDRAWALFRALDGKGLVPDGYVEGWKKTFEEDFSPRRGAELVARAWTDPEFRQLLLTDGTAAVAQYGYLGPQGEYIVAVEDTPTLKNVIVCSLcScTAWPILGLPPTWYKSFEYRARVVREPRKVLSEMGTEIASDIEIRVYDTTAETRYMVLPQRPAGTEGWSQEQLQEIVTKDCLIGVAIPQVPT 205
                                    18        28        38        48        58        68        78        88        98       108   | | 118       128       138       148       158       168       178       188       198       
                                                                                                                                 112-CSD                                                                                         
                                                                                                                                   114-CSO

Chain B from PDB  Type:PROTEIN  Length:212
 aligned with NHAB_RHOER | P13449 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  
           NHAB_RHOER     1 MDGVHDLAGVQGFGKVPHTVNADIGPTFHAEWEHLPYSLMFAGVAELGAFSVDEVRYVVERMEPRHYMMTPYYERYVIGVATLMVEKGILTQDELESLAGGPFPLSRPSESEGRPAPVETTTFEVGQRVRVRDEYVPGHIRMPAYCRGRVGTISHRTTEKWPFPDAIGHGRNDAGEEPTYHVKFAAEELFGSDTDGGSVVVDLFEGYLEPAA 212
               SCOP domains d2cz6b_ B: Iron-containing nitrile hydratase                                                                                                                                                                         SCOP domains
               CATH domains 2cz6B01 B:1-110  [code=1.10.472.20, no name defined]                                                          2cz6B02 B:111-212  [code=2.30.30.50, no name defined]                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................hhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...........................eeee...........hhhhh..eeeeeee......hhhhhh..........eeeeeeehhhhhh......eeeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------V---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cz6 B   1 MDGVHDLAGVQGFGKVPHTVNADIGPTFHAEWEHLPYSLMFAGVAELGAFSVDEVRYVVERMEPRHYMMTPYYERYVIGVATLMVEKGILTQDELESLAGGPFPLSRPSESEGRPAPVETTTFEVGQRVRVRDEYVPGHIRMPAYCRGRVGTISHRTTEKWPFPDAIGHGRNDAGEEPTYHVKFAAEELFGSDTDGGSVVVDLFEGYLEPAA 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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 '\|'

(no "Pfam Domain" information available for 2CZ6)

Asymmetric Unit(hide GO term definitions)

Chain A (NHAA_RHOER | P13448)

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:0080109	indole-3-acetonitrile nitrile hydratase activity	Catalysis of the reaction: indole-3-acetonitrile + H2O = indole-3-acetamide.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0018822	nitrile hydratase activity	Catalysis of the reaction: an aliphatic amide = a nitrile + H2O.
	GO:0046914	transition metal ion binding	Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
biological process
	GO:0006807	nitrogen compound metabolic process	The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.

Chain B (NHAB_RHOER | P13449)

molecular function
	GO:0080109	indole-3-acetonitrile nitrile hydratase activity	Catalysis of the reaction: indole-3-acetonitrile + H2O = indole-3-acetamide.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0018822	nitrile hydratase activity	Catalysis of the reaction: an aliphatic amide = a nitrile + H2O.
	GO:0046914	transition metal ion binding	Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
biological process
	GO:0006807	nitrogen compound metabolic process	The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.

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2cz7	FE-TYPE NHASE PHOTO-ACTIVATED FOR 75MIN AT 105K RELATED ID: AR_001000506.2 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 9)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

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