2JI9 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

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Title :   X-RAY STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH 3-DEAZA-THDP

Authors :   C. L. Berthold, C. G. Toyota, P. Moussatche, M. D. Wood, F. Leeper, N. G. J. Richards, Y. Lindqvist

Date :   26 Feb 07 (Deposition) - 17 Jul 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Oxalate Degradation, Thiamine Pyrophosphate, Lyase, Flavoprotein, Decarboxylase, Cofactor Analogue Inhibitor Complex, Non- Oxidative Decarboxylase, Thiamin Diphosphate-Dependent (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. L. Berthold, C. G. Toyota, P. Moussatche, M. D. Wood, F. Leeper, N. G. J. Richards, Y. Lindqvist
Crystallographic Snapshots Of Oxalyl-Coa Decarboxylase Give Insights Into Catalysis By Nonoxidative Thdp-Dependent Decarboxylases
Structure V. 15 853 2007
PubMed-ID: 17637344 | Reference-DOI: 10.1016/J.STR.2007.06.001

Molecule 1 - OXALYL-COA DECARBOXYLASE
	Chains	:	A, B
	EC Number	:	4.1.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET9A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	OXALOBACTER FORMIGENES
	Organism Taxid	:	847
	Synonym	:	OXALYL-COENZYMEA DECARBOXYLASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	B3P	2	Ligand/Ion	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	TPW	2	Ligand/Ion	2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGENDIPHOSPHATE

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	ADP	4	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	B3P	4	Ligand/Ion	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	TPW	4	Ligand/Ion	2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGENDIPHOSPHATE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:32 , GLU A:56 , ASN A:86 , GLU A:121 , TYR B:377 , GLY B:400 , ALA B:401 , ASN B:402 , ALA B:403 , GLY B:426 , MET B:428 , GLY B:451 , ASP B:452 , SER B:453 , ALA B:454 , PHE B:457 , ASN B:479 , GLY B:481 , ILE B:482 , TYR B:483 , MG B:1555 , HOH B:2251 , HOH B:2269	BINDING SITE FOR RESIDUE TPW B1554
2	AC2	SOFTWARE	TYR A:377 , GLY A:400 , ALA A:401 , ASN A:402 , ALA A:403 , GLY A:426 , MET A:428 , GLY A:451 , ASP A:452 , SER A:453 , ALA A:454 , PHE A:457 , ASN A:479 , GLY A:481 , ILE A:482 , TYR A:483 , MG A:1555 , HOH A:2245 , HOH A:2250 , VAL B:32 , GLU B:56 , VAL B:79 , ASN B:86 , GLU B:121	BINDING SITE FOR RESIDUE TPW A1554
3	AC3	SOFTWARE	ASP B:452 , ASN B:479 , GLY B:481 , TPW B:1554 , HOH B:2269	BINDING SITE FOR RESIDUE MG B1555
4	AC4	SOFTWARE	ASP A:452 , ASN A:479 , GLY A:481 , TPW A:1554 , HOH A:2250	BINDING SITE FOR RESIDUE MG A1555
5	AC5	SOFTWARE	ARG B:160 , GLY B:221 , LYS B:222 , GLY B:223 , TYR B:226 , MET B:247 , GLY B:280 , ALA B:281 , ARG B:282 , ASP B:306 , ILE B:307 , GLY B:324 , ASP B:325 , ILE B:326 , HOH B:2311 , HOH B:2312	BINDING SITE FOR RESIDUE ADP B1556
6	AC6	SOFTWARE	ARG A:160 , GLY A:221 , LYS A:222 , GLY A:223 , MET A:247 , GLY A:280 , ALA A:281 , ARG A:282 , LEU A:286 , ASP A:306 , ILE A:307 , GLY A:324 , ASP A:325 , ILE A:326 , HOH A:2244 , HOH A:2300 , HOH A:2301 , HOH A:2302	BINDING SITE FOR RESIDUE ADP A1556
7	AC7	SOFTWARE	ASP A:489 , GLY A:493 , VAL A:494 , ARG A:499	BINDING SITE FOR RESIDUE B3P A1557
8	AC8	SOFTWARE	ASP B:489 , GLY B:493 , ARG B:499	BINDING SITE FOR RESIDUE B3P B1557

(no "SS Bond" information available for 2JI9)

Asymmetric Unit

No.	Residues
1	Ile A:34	-	Pro A:35
2	Ile B:34	-	Pro B:35

(no "SAP(SNP)/Variant" information available for 2JI9)

(no "PROSITE Motif" information available for 2JI9)

(no "Exon" information available for 2JI9)

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:547
 aligned with OXC_OXAFO | P40149 from UniProtKB/Swiss-Prot  Length:568

    Alignment length:547
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       
            OXC_OXAFO     7 VELTDGFHVLIDALKMNDIDTMYGVVGIPITNLARMWQDDGQRFYSFRHEQHAGYAASIAGYIEGKPGVCLTVSAPGFLNGVTSLAHATTNCFPMILLSGSSEREIVDLQQGDYEEMDQMNVARPHCKASFRINSIKDIPIGIARAVRTAVSGRPGGVYVDLPAKLFGQTISVEEANKLLFKPIDPAPAQIPAEDAIARAADLIKNAKRPVIMLGKGAAYAQCDDEIRALVEETGIPFLPMGMAKGLLPDNHPQSAAATRAFALAQCDVCVLIGARLNWLMQHGKGKTWGDELKKYVQIDIQANEMDSNQPIAAPVVGDIKSAVSLLRKALKGAPKADAEWTGALKAKVDGNKAKLAGKMTAETPSGMMNYSNSLGVVRDFMLANPDISLVNEGANALDNTRMIVDMLKPRKRLDSGTWGVMGIGMGYCVAAAAVTGKPVIAVEGDSAFGFSGMELETICRYNLPVTVIIMNNGGIYKGNEADPQPGVISCTRLTRGRYDMMMEAFGGKGYVANTPAELKAALEEAVASGKPCLINAMIDPDAGVES 553
               SCOP domains d2ji9a2 A:7-194 Oxalyl-CoA decarboxylase                                                                                                                                                    d2ji9a1 A:195-369 Oxalyl-CoA decarboxylase                                                                                                                                     d2ji9a3 A:370-553 Oxalyl-CoA decarboxylase                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhh...eeee.....hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhh.........hhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhh....eeeeeee.hhh..eeehhhhhhhh............hhhhhhhhhhhhhh....eeeehhhhhhh.hhhhhhhhhhhhh..eee...............hhhhhhhhhhhh.eeeee....hhhhhhhhhhhhh....eeeeee.hhhhh.......eeee.hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhh.......ee.........hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhh...eeeeeee.........................hhhhhhhh...eeeee.hhhhhhhhhhhhhhhh..eeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ji9 A   7 VELTDGFHVLIDALKMNDIDTMYGVVGIPITNLARMWQDDGQRFYSFRHEQHAGYAASIAGYIEGKPGVCLTVSAPGFLNGVTSLAHATTNCFPMILLSGSSEREIVDLQQGDYEEMDQMNVARPHCKASFRINSIKDIPIGIARAVRTAVSGRPGGVYVDLPAKLFGQTISVEEANKLLFKPIDPAPAQIPAEDAIARAADLIKNAKRPVIMLGKGAAYAQCDDEIRALVEETGIPFLPMGMAKGLLPDNHPQSAAATRAFALAQCDVCVLIGARLNWLMQHGKGKTWGDELKKYVQIDIQANEMDSNQPIAAPVVGDIKSAVSLLRKALKGAPKADAEWTGALKAKVDGNKAKLAGKMTAETPSGMMNYSNSLGVVRDFMLANPDISLVNEGANALDNTRMIVDMLKPRKRLDSGTWGVMGIGMGYCVAAAAVTGKPVIAVEGDSAFGFSGMELETICRYNLPVTVIIMNNGGIYKGNEADPQPGVISCTRLTRGRYDMMMEAFGGKGYVANTPAELKAALEEAVASGKPCLINAMIDPDAGVES 553
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546

Chain B from PDB  Type:PROTEIN  Length:547
 aligned with OXC_OXAFO | P40149 from UniProtKB/Swiss-Prot  Length:568

    Alignment length:547
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       
            OXC_OXAFO     7 VELTDGFHVLIDALKMNDIDTMYGVVGIPITNLARMWQDDGQRFYSFRHEQHAGYAASIAGYIEGKPGVCLTVSAPGFLNGVTSLAHATTNCFPMILLSGSSEREIVDLQQGDYEEMDQMNVARPHCKASFRINSIKDIPIGIARAVRTAVSGRPGGVYVDLPAKLFGQTISVEEANKLLFKPIDPAPAQIPAEDAIARAADLIKNAKRPVIMLGKGAAYAQCDDEIRALVEETGIPFLPMGMAKGLLPDNHPQSAAATRAFALAQCDVCVLIGARLNWLMQHGKGKTWGDELKKYVQIDIQANEMDSNQPIAAPVVGDIKSAVSLLRKALKGAPKADAEWTGALKAKVDGNKAKLAGKMTAETPSGMMNYSNSLGVVRDFMLANPDISLVNEGANALDNTRMIVDMLKPRKRLDSGTWGVMGIGMGYCVAAAAVTGKPVIAVEGDSAFGFSGMELETICRYNLPVTVIIMNNGGIYKGNEADPQPGVISCTRLTRGRYDMMMEAFGGKGYVANTPAELKAALEEAVASGKPCLINAMIDPDAGVES 553
               SCOP domains d2ji9b2 B:7-194 Oxalyl-CoA decarboxylase                                                                                                                                                    d2ji9b1 B:195-369 Oxalyl-CoA decarboxylase                                                                                                                                     d2ji9b3 B:370-553 Oxalyl-CoA decarboxylase                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---TPP_enzyme_N-2ji9B05 B:10-181                                                                                                                                               ---------------------TPP_enzyme_M-2ji9B01 B:203-335                                                                                                       ----------------------------------------------------------------TPP_enzyme_C-2ji9B03 B:400-543                                                                                                                  ---------- Pfam domains (1)
           Pfam domains (2) ---TPP_enzyme_N-2ji9B06 B:10-181                                                                                                                                               ---------------------TPP_enzyme_M-2ji9B02 B:203-335                                                                                                       ----------------------------------------------------------------TPP_enzyme_C-2ji9B04 B:400-543                                                                                                                  ---------- Pfam domains (2)
         Sec.struct. author ..eeehhhhhhhhhhhh...eeee.....hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhh........hhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhh....eeeeeee.hhh..eeehhhhhhhh............hhhhhhhhhhhhhh...eeeeehhhhhhh.hhhhhhhhhhhhh..eee...............hhhhhhhhhhhh.eeeee....hhhhhhhhhhhhh....eeeeee.hhhhh.......eeee.hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhh.......eee........hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhh...eeeeeee.........................hhhhhhhh...eeeee.hhhhhhhhhhhhhhhh..eeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ji9 B   7 VELTDGFHVLIDALKMNDIDTMYGVVGIPITNLARMWQDDGQRFYSFRHEQHAGYAASIAGYIEGKPGVCLTVSAPGFLNGVTSLAHATTNCFPMILLSGSSEREIVDLQQGDYEEMDQMNVARPHCKASFRINSIKDIPIGIARAVRTAVSGRPGGVYVDLPAKLFGQTISVEEANKLLFKPIDPAPAQIPAEDAIARAADLIKNAKRPVIMLGKGAAYAQCDDEIRALVEETGIPFLPMGMAKGLLPDNHPQSAAATRAFALAQCDVCVLIGARLNWLMQHGKGKTWGDELKKYVQIDIQANEMDSNQPIAAPVVGDIKSAVSLLRKALKGAPKADAEWTGALKAKVDGNKAKLAGKMTAETPSGMMNYSNSLGVVRDFMLANPDISLVNEGANALDNTRMIVDMLKPRKRLDSGTWGVMGIGMGYCVAAAAVTGKPVIAVEGDSAFGFSGMELETICRYNLPVTVIIMNNGGIYKGNEADPQPGVISCTRLTRGRYDMMMEAFGGKGYVANTPAELKAALEEAVASGKPCLINAMIDPDAGVES 553
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546

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 "CATH Domain" information available for 2JI9)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: FAD_DHS (82)

Family: TPP_enzyme_M (50)

Oxalobacter formigenes (4)

1a	TPP_enzyme_M-2ji9B01	B:203-335
1b	TPP_enzyme_M-2ji9B02	B:203-335

Clan: THDP-binding (106)

Family: TPP_enzyme_C (54)

Oxalobacter formigenes (4)

2a	TPP_enzyme_C-2ji9B03	B:400-543
2b	TPP_enzyme_C-2ji9B04	B:400-543

Family: TPP_enzyme_N (54)

Oxalobacter formigenes (4)

3a	TPP_enzyme_N-2ji9B05	B:10-181
3b	TPP_enzyme_N-2ji9B06	B:10-181

Asymmetric Unit(hide GO term definitions)

Chain A,B (OXC_OXAFO | P40149)

molecular function
	GO:0043531	ADP binding	Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate.
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	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: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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0008949	oxalyl-CoA decarboxylase activity	Catalysis of the reaction: H(+) + oxalyl-CoA = CO(2) + formyl-CoA.
	GO:0030976	thiamine pyrophosphate binding	Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
biological process
	GO:0033611	oxalate catabolic process	The chemical reactions and pathways resulting in the breakdown of oxalate, the organic acid ethanedioate.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ile A:34 - Pro A:35	[ RasMol ]
		Ile B:34 - Pro B:35	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Access by PDB/NDB ID
	2ji9
		Family and Domain Information	:	ProDom \| SYSTERS
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Access by UniProt ID/Accession number
	OXC_OXAFO \| P40149
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	4.1.1.8
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		Domain Information	:	XDom
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	OXC_OXAFO \| P40149
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UniProtKB/Swiss-Prot
	OXC_OXAFO \| P40149	:	2c31 2ji6 2ji7 2ji8 2jib

2c31	CRYSTAL STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH THE COFACTOR DERIVATIVE THIAMIN-2-THIAZOLONE DIPHOSPHATE AND ADENOSINE DIPHOSPHATE
2ji6	X-RAY STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH 3-DEAZA-THDP AND OXALYL -COA
2ji7	X-RAY STRUCTURE OF OXALYL-COA DECARBOXYLASE WITH COVALENT REACTION INTERMEDIATE
2ji8	X-RAY STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH FORMYL-COA
2jib	X-RAY STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH COENZYME-A

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 6)

CATH Domains (0, 0)

Pfam Domains (3, 6)

Gene Ontology (10, 10)

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Related Entries Specified in the PDB File