1F0X - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF D-LACTATE DEHYDROGENASE, A PERIPHERAL MEMBRANE RESPIRATORY ENZYME.

Authors :   O. Dym, E. A. Pratt, C. Ho, D. Eisenberg

Date :   17 May 00 (Deposition) - 23 Aug 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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 :   O. Dym, E. A. Pratt, C. Ho, D. Eisenberg
The Crystal Structure Of D-Lactate Dehydrogenase, A Peripheral Membrane Respiratory Enzyme.
Proc. Natl. Acad. Sci. Usa V. 97 9413 2000
PubMed-ID: 10944213 | Reference-DOI: 10.1073/PNAS.97.17.9413
(for further references see the PDB file header)

Molecule 1 - D-LACTATE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.1.28
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	DLDH

		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 (1, 2)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:39 , LEU A:73 , MET A:74 , ALA A:76 , ALA A:77 , ASN A:78 , THR A:79 , GLY A:80 , LEU A:81 , GLY A:84 , SER A:85 , ILE A:142 , GLY A:143 , SER A:144 , SER A:150 , ILE A:152 , CYS A:156 , SER A:159 , GLY A:160 , ALA A:257 , GLY A:258 , LEU A:260 , VAL A:262 , GLU A:528 , HIS A:529 , ASN A:555 , HOH A:2001 , HOH A:2016 , HOH A:2040 , HOH A:2297	BINDING SITE FOR RESIDUE FAD A 600
2	AC2	SOFTWARE	PHE B:1039 , MET B:1074 , ALA B:1076 , ALA B:1077 , ASN B:1078 , THR B:1079 , GLY B:1080 , LEU B:1081 , GLY B:1084 , SER B:1085 , ILE B:1142 , GLY B:1143 , SER B:1144 , SER B:1150 , ILE B:1152 , GLY B:1153 , CYS B:1156 , SER B:1159 , GLY B:1160 , ALA B:1257 , GLY B:1258 , LEU B:1260 , ALA B:1261 , VAL B:1262 , GLU B:1528 , HIS B:1529 , ASN B:1555 , HOH B:2005 , HOH B:2007 , HOH B:2027 , HOH B:2060	BINDING SITE FOR RESIDUE FAD B 1600

(no "SS Bond" information available for 1F0X)

Asymmetric Unit

No.	Residues
1	Leu A:377	-	Pro A:378
2	Leu B:1377	-	Pro B:1378

(no "SAP(SNP)/Variant" information available for 1F0X)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FAD_PCMH	PS51387	PCMH-type FAD-binding domain profile.	DLD_ECOLI	42-213	2	A:42-213 B:1042-1213

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FAD_PCMH	PS51387	PCMH-type FAD-binding domain profile.	DLD_ECOLI	42-213	1	A:42-213 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FAD_PCMH	PS51387	PCMH-type FAD-binding domain profile.	DLD_ECOLI	42-213	1	- B:1042-1213

(no "Exon" information available for 1F0X)

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:502
 aligned with DLD_ECOLI | P06149 from UniProtKB/Swiss-Prot  Length:571

    Alignment length:559
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558         
           DLD_ECOLI      9 NKAFLNELARLVGSSHLLTDPAKTARYRKGFRSGQGDALAVVFPGSLLELWRVLKACVTADKIILMQAANTGLTEGSTPNGNDYDRDVVIISTLRLDKLHVLGKGEQVLAYPGTTLYSLEKALKPLGREPHSVIGSSCIGASVIGGICNNSGGSLVQRGPAYTEMSLFARINEDGKLTLVNHLGIDLGETPEQILSKLDDDRIKDDDVRHDGRHAHDYDYVHRVRDIEADTPARYNADPDRLFESSGCAGKLAVFAVRLDTFEAEKNQQVFYIGTNQPEVLTEIRRHILANFENLPVAGEYMHRDIYDIAEKYGKDTFLMIDKLGTDKMPFFFNLKGRTDAMLEKVKFFRPHFTDRAMQKFGHLFPSHLPPRMKNWRDKYEHHLLLKMAGDGVGEAKSWLVDYFKQAEGDFFVCTPEEGSKAFLHRFAAAGAAIRYQAVHSDEVEDILALDIALRRNDTEWYEHLPPEIDSQLVHKLYYGHFMCYVFHQDYIVKKGVDVHALKEQMLELLQQRGAQYPAEHNVGHLYKAPETLQKFYRENDPTNSMNPGIGKTSKRKNW  567
               SCOP domains d1f0xa2 A:9-273 D-lactate dehydrogenase                                                                                                                                                                                                                                  d1f0xa1 A:274-567 D-lactate dehydrogenase                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1f0xA02 A:9-105,A:520-567 Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2   1f0xA03 A:106-268  [code=3.30.465.10, no name defined]                                                                                                             1f0xA01 A:269-310,A:377-434               ------------------------------------------------------------------1f0xA01 A:269-310,A:377-434                               1f0xA04 A:435-519  [code=3.30.1370.20, no name defined]                              1f0xA02 A:9-105,A:520-567                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...ee.hhhhhhhhhh..........eee...hhhhhhhhhhhhhhh..eeeee....................eeeee......eeee....eeee....hhhhhhhhhh...ee....hhhhhhh.hhhhhhhh................eeeeee.....eeeee........hhhhhhhhhhh...hhhh...........hhhhhhhh...........hhhhh..........eeeeeeee.ee.....eeeeeee.hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhh---------------------------------------------------------.hhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee............hhhhhh.eeeeeeeee....eeeeeeeee...hhhhhhhhhhhhhhhh................hhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------FAD_PCMH  PDB: A:42-213 UniProt: 42-213                                                                                                                                     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1f0x A    9 NKAFLNELARLVGSSHLLTDPAKTARYRKGFRSGQGDALAVVFPGSLLELWRVLKACVTADKIILMQAANTGLTEGSTPNGNDYDRDVVIISTLRLDKLHVLGKGEQVLAYPGTTLYSLEKALKPLGREPHSVIGSSCIGASVIGGICNNSGGSLVQRGPAYTEMSLFARINEDGKLTLVNHLGIDLGETPEQILSKLDDDRIKDDDVRHDGRHAHDYDYVHRVRDIEADTPARYNADPDRLFESSGCAGKLAVFAVRLDTFEAEKNQQVFYIGTNQPEVLTEIRRHILANFENLPVAGEYMHRDIYDIAE---------------------------------------------------------LPPRMKNWRDKYEHHLLLKMAGDGVGEAKSWLVDYFKQAEGDFFVCTPEEGSKAFLHRFAAAGAAIRYQAVHSDEVEDILALDIALRRNDTEWYEHLPPEIDSQLVHKLYYGHFMCYVFHQDYIVKKGVDVHALKEQMLELLQQRGAQYPAEHNVGHLYKAPETLQKFYRENDPTNSMNPGIGKTSKRKNW  567
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318|        -         -         -         -         -       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558         
                                                                                                                                                                                                                                                                                                                                                319                                                       377

Chain B from PDB  Type:PROTEIN  Length:502
 aligned with DLD_ECOLI | P06149 from UniProtKB/Swiss-Prot  Length:571

    Alignment length:559
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558         
           DLD_ECOLI      9 NKAFLNELARLVGSSHLLTDPAKTARYRKGFRSGQGDALAVVFPGSLLELWRVLKACVTADKIILMQAANTGLTEGSTPNGNDYDRDVVIISTLRLDKLHVLGKGEQVLAYPGTTLYSLEKALKPLGREPHSVIGSSCIGASVIGGICNNSGGSLVQRGPAYTEMSLFARINEDGKLTLVNHLGIDLGETPEQILSKLDDDRIKDDDVRHDGRHAHDYDYVHRVRDIEADTPARYNADPDRLFESSGCAGKLAVFAVRLDTFEAEKNQQVFYIGTNQPEVLTEIRRHILANFENLPVAGEYMHRDIYDIAEKYGKDTFLMIDKLGTDKMPFFFNLKGRTDAMLEKVKFFRPHFTDRAMQKFGHLFPSHLPPRMKNWRDKYEHHLLLKMAGDGVGEAKSWLVDYFKQAEGDFFVCTPEEGSKAFLHRFAAAGAAIRYQAVHSDEVEDILALDIALRRNDTEWYEHLPPEIDSQLVHKLYYGHFMCYVFHQDYIVKKGVDVHALKEQMLELLQQRGAQYPAEHNVGHLYKAPETLQKFYRENDPTNSMNPGIGKTSKRKNW  567
               SCOP domains d1f0xb2 B:1009-1273 D-lactate dehydrogenase                                                                                                                                                                                                                              d1f0xb1 B:1274-1567 D-lactate dehydrogenase                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1f0xB02 B:1009-1105,B:1520-1566                                                                  1f0xB03 B:1106-1268  [code=3.30.465.10, no name defined]                                                                                                           1f0xB01 B:1269-1310,B:1377-1434           ------------------------------------------------------------------1f0xB01 B:1269-1310,B:1377-1434                           1f0xB04 B:1435-1519  [code=3.30.1370.20, no name defined]                            1f0xB02 B:1009-1105,B:1520-1566                - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...ee.hhhhhhhhhh..........eee...hhhhhhhhhhhhhhh..eeeee....................eeeee......eeee....eeee....hhhhhhhhhh...ee......hhhhh.hhhhhhhhh...............eeeeee.....eeeee........hhhhhhhhhhh...hhhh...........hhhhhhhh...........hhhhh..........eeeeeeee.ee.....eeeeeee.hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhh---------------------------------------------------------.hhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee............hhhhhh.eeeeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhh...............hhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------FAD_PCMH  PDB: B:1042-1213 UniProt: 42-213                                                                                                                                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1f0x B 1009 NKAFLNELARLVGSSHLLTDPAKTARYRKGFRSGQGDALAVVFPGSLLELWRVLKACVTADKIILMQAANTGLTEGSTPNGNDYDRDVVIISTLRLDKLHVLGKGEQVLAYPGTTLYSLEKALKPLGREPHSVIGSSCIGASVIGGICNNSGGSLVQRGPAYTEMSLFARINEDGKLTLVNHLGIDLGETPEQILSKLDDDRIKDDDVRHDGRHAHDYDYVHRVRDIEADTPARYNADPDRLFESSGCAGKLAVFAVRLDTFEAEKNQQVFYIGTNQPEVLTEIRRHILANFENLPVAGEYMHRDIYDIAE---------------------------------------------------------LPPRMKNWRDKYEHHLLLKMAGDGVGEAKSWLVDYFKQAEGDFFVCTPEEGSKAFLHRFAAAGAAIRYQAVHSDEVEDILALDIALRRNDTEWYEHLPPEIDSQLVHKLYYGHFMCYVFHQDYIVKKGVDVHALKEQMLELLQQRGAQYPAEHNVGHLYKAPETLQKFYRENDPTNSMNPGIGKTSKRKNW 1567
                                  1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188      1198      1208      1218      1228      1238      1248      1258      1268      1278      1288      1298      1308      1318|        -         -         -         -         -      1378      1388      1398      1408      1418      1428      1438      1448      1458      1468      1478      1488      1498      1508      1518      1528      1538      1548      1558         
                                                                                                                                                                                                                                                                                                                                               1319                                                      1377

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 1F0X)

Asymmetric Unit(hide GO term definitions)

Chain A,B (DLD_ECOLI | P06149)

molecular function
	GO:0008720	D-lactate dehydrogenase activity	Catalysis of the reaction: (R)-lactate + NAD(+) = H(+) + NADH + pyruvate.
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	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:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	GO:0004457	lactate dehydrogenase activity	Catalysis of the reaction: lactate + NAD+ = H+ + NADH + pyruvate.
	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:0016614	oxidoreductase activity, acting on CH-OH group of donors	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
	GO:0016901	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule.
biological process
	GO:0009060	aerobic respiration	The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
	GO:0009061	anaerobic respiration	The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.
	GO:0006089	lactate metabolic process	The chemical reactions and pathways involving lactate, the anion of lactic acid.
	GO:0019516	lactate oxidation	The chemical reactions and pathways resulting in the conversion of lactate to other compounds, such as pyruvate, with concomitant loss of electrons.
	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.
	GO:0022904	respiratory electron transport chain	A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
cellular component
	GO:0031234	extrinsic component of cytoplasmic side of plasma membrane	The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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