1V6A - JenaLib

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Title :   CRYSTAL STRUCTURE OF L-LACTATE DEHYDROGENASE FROM CYPRINUS CARPIO

Authors :   K. Watanabe, H. Motoshima

Date :   28 Nov 03 (Deposition) - 15 Feb 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   L-Lactate Dehydrogenase, Cyprinus Carpio, Nadh, M-Type, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Watanabe, H. Motoshima
Crystal Structure Of L-Lactate Dehydrogenase From Cyprinus Carpio
To Be Published
PubMed: search

Molecule 1 - L-LACTATE DEHYDROGENASE A CHAIN
	Chains	:	A, B
	EC Number	:	1.1.1.27
	Organism Common	:	COMMON CARP
	Organism Scientific	:	CYPRINUS CARPIO
	Organism Taxid	:	7962
	Synonym	:	LDH
	Tissue	:	SKELETAL MUSCLE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	TRE	4	Ligand/Ion	TREHALOSE

Biological Unit 1 (1, 8)

No.	Name	Count	Type	Full Name
1	TRE	8	Ligand/Ion	TREHALOSE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:22 , GLU A:47 , LYS A:76 , VAL A:78 , SER A:84 , VAL A:85 , ALA A:87 , HOH A:388 , HOH A:433	BINDING SITE FOR RESIDUE TRE A 333
2	AC2	SOFTWARE	VAL A:28 , GLY A:29 , ASP A:52 , ALA A:96 , GLY A:97 , ARG A:99 , HOH A:335	BINDING SITE FOR RESIDUE TRE A 334
3	AC3	SOFTWARE	LYS B:22 , GLU B:47 , LYS B:76 , VAL B:78 , SER B:84 , VAL B:85 , HOH B:403 , HOH B:460	BINDING SITE FOR RESIDUE TRE B 333
4	AC4	SOFTWARE	GLY B:29 , ASP B:52 , VAL B:53 , LYS B:57 , ALA B:96 , GLY B:97 , ARG B:99 , HOH B:418 , HOH B:456	BINDING SITE FOR RESIDUE TRE B 334

(no "SS Bond" information available for 1V6A)

Asymmetric Unit

No.	Residues
1	Asn A:138	-	Pro A:139
2	Asn B:138	-	Pro B:139

(no "SAP(SNP)/Variant" information available for 1V6A)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	L_LDH	PS00064	L-lactate dehydrogenase active site.	LDHA_CYPCA	191-197	2	A:190-196 B:190-196

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	L_LDH	PS00064	L-lactate dehydrogenase active site.	LDHA_CYPCA	191-197	4	A:190-196 B:190-196

(no "Exon" information available for 1V6A)

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:332
 aligned with LDHA_CYPCA | Q9W7K5 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:332
                                    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  
           LDHA_CYPCA     2 ASTKEKLITHVSKEEPAGPTNKVTVVGVGMVGMAAAISILLKDLTDELALVDVMEDKLKGEAMDLQHGSLFLKTHKIVADKDYSVTANSKVVVVTAGARQQEGESRLNLVQRNVNIFKFIIPNIIKYSPNCILLVVSNPVDILTYVAWKLSGLPRNRVIGSGTNLDSARFRHLMGEKLGIHPSNCHGWVIGEHGDSSVPVWSGVNVAGVFLQGLNPDMGTDKDKEDWKSVHKMVVDSAYEVIKLKGYTSWAIGMSAADLCQSILKNLRKCHPVSTLVKGMHGVNEEVFLSVPCILGNSGLTDVVHMTLKSDEEKQLVKSAETLWGVQKDLTL 333
               SCOP domains d1v6aa1 A:1-160 automated matches                                                                                                                               d1v6aa2 A:161-332 automated matches                                                                                                                                          SCOP domains
               CATH domains --------------1v6aA01 A:15-162 NAD(P)-binding Rossmann-like Domain                                                                                                1v6aA02 A:163-330 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                             -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..............eeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh...eeee..hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhh.ee..eee.....eee.hhh.ee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v6a A   1 ASTKEKLITHVSKEEPAGPTNKVTVVGVGMVGMAAAISILLKDLTDELALVDVMEDKLKGEAMDLQHGSLFLKTHKIVADKDYSVTANSKVVVVTAGARQQEGESRLNLVQRNVNIFKFIIPNIIKYSPNCILLVVSNPVDILTYVAWKLSGLPRNRVIGSGTNLDSARFRHLMGEKLGIHPSNCHGWVIGEHGDSSVPVWSGVNVAGVFLQGLNPDMGTDKDKEDWKSVHKMVVDSAYEVIKLKGYTSWAIGMSAADLCQSILKNLRKCHPVSTLVKGMHGVNEEVFLSVPCILGNSGLTDVVHMTLKSDEEKQLVKSAETLWGVQKDLTL 332
                                    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       310       320       330

Chain B from PDB  Type:PROTEIN  Length:332
 aligned with LDHA_CYPCA | Q9W7K5 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:332
                                    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  
           LDHA_CYPCA     2 ASTKEKLITHVSKEEPAGPTNKVTVVGVGMVGMAAAISILLKDLTDELALVDVMEDKLKGEAMDLQHGSLFLKTHKIVADKDYSVTANSKVVVVTAGARQQEGESRLNLVQRNVNIFKFIIPNIIKYSPNCILLVVSNPVDILTYVAWKLSGLPRNRVIGSGTNLDSARFRHLMGEKLGIHPSNCHGWVIGEHGDSSVPVWSGVNVAGVFLQGLNPDMGTDKDKEDWKSVHKMVVDSAYEVIKLKGYTSWAIGMSAADLCQSILKNLRKCHPVSTLVKGMHGVNEEVFLSVPCILGNSGLTDVVHMTLKSDEEKQLVKSAETLWGVQKDLTL 333
               SCOP domains d1v6ab1 B:1-160 automated matches                                                                                                                               d1v6ab2 B:161-332 automated matches                                                                                                                                          SCOP domains
               CATH domains --------------1v6aB01 B:15-162 NAD(P)-binding Rossmann-like Domain                                                                                                1v6aB02 B:163-330 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                             -- CATH domains
           Pfam domains (1) --------------------Ldh_1_N-1v6aB03 B:21-161                                                                                                                     -Ldh_1_C-1v6aB01 B:163-330                                                                                                                                               -- Pfam domains (1)
           Pfam domains (2) --------------------Ldh_1_N-1v6aB04 B:21-161                                                                                                                     -Ldh_1_C-1v6aB02 B:163-330                                                                                                                                               -- Pfam domains (2)
         Sec.struct. author .hhhhhhh..............eeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh...eeee..hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v6a B   1 ASTKEKLITHVSKEEPAGPTNKVTVVGVGMVGMAAAISILLKDLTDELALVDVMEDKLKGEAMDLQHGSLFLKTHKIVADKDYSVTANSKVVVVTAGARQQEGESRLNLVQRNVNIFKFIIPNIIKYSPNCILLVVSNPVDILTYVAWKLSGLPRNRVIGSGTNLDSARFRHLMGEKLGIHPSNCHGWVIGEHGDSSVPVWSGVNVAGVFLQGLNPDMGTDKDKEDWKSVHKMVVDSAYEVIKLKGYTSWAIGMSAADLCQSILKNLRKCHPVSTLVKGMHGVNEEVFLSVPCILGNSGLTDVVHMTLKSDEEKQLVKSAETLWGVQKDLTL 332
                                    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       310       320       330

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Common carp (Cyprinus carpio) (1)

1a	1v6aA01	A:15-162
1b	1v6aB01	B:15-162

Architecture: Alpha-Beta Complex (3881)

Topology: L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 (116)

Homologous Superfamily: L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2 (116)

Common carp (Cyprinus carpio) (1)

2a	1v6aA02	A:163-330
2b	1v6aB02	B:163-330

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: LDH_C (56)

Family: Ldh_1_C (51)

Cyprinus carpio (Common carp) (1)

1a	Ldh_1_C-1v6aB01	B:163-330
1b	Ldh_1_C-1v6aB02	B:163-330

Clan: NADP_Rossmann (1239)

Family: Ldh_1_N (51)

Cyprinus carpio (Common carp) (1)

2a	Ldh_1_N-1v6aB03	B:21-161
2b	Ldh_1_N-1v6aB04	B:21-161

Asymmetric Unit(hide GO term definitions)

Chain A,B (LDHA_CYPCA | Q9W7K5)

molecular function
	GO:0004459	L-lactate dehydrogenase activity	Catalysis of the reaction: (S)-lactate + NAD+ = pyruvate + NADH + H+.
	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: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.
	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0019752	carboxylic acid metabolic process	The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	Cis Peptide Bonds
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Biological Unit
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6ldh	DOGFISH M4 APO-LACTATE DEHYDROGENASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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