3JTM - JenaLib

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:354 , PRO A:362 , HOH A:432 , HOH A:580 , HOH A:590 , HOH A:671	BINDING SITE FOR RESIDUE SO4 A 1
02	AC2	SOFTWARE	LYS A:45 , TYR A:184 , ARG A:185	BINDING SITE FOR RESIDUE SO4 A 3
03	AC3	SOFTWARE	TYR A:102 , THR A:104 , LYS A:204 , LEU A:223 , MET A:225 , ALA A:226 , LEU A:229 , HOH A:459 , HOH A:635	BINDING SITE FOR RESIDUE GOL A 4
04	AC4	SOFTWARE	HOH A:7 , VAL A:53 , GLU A:54 , ASN A:55 , ALA A:56 , ARG A:60	BINDING SITE FOR RESIDUE GOL A 5
05	AC5	SOFTWARE	PRO A:97 , PHE A:98 , GLY A:121 , ILE A:122 , ASN A:146 , GLY A:335 , TYR A:344 , HOH A:400 , HOH A:403 , HOH A:622 , HOH A:756	BINDING SITE FOR RESIDUE GOL A 8
06	AC6	SOFTWARE	LEU A:57 , GLY A:58 , LYS A:349 , GOL A:386 , HOH A:437 , HOH A:475 , HOH A:484 , HOH A:492	BINDING SITE FOR RESIDUE GOL A 9
07	AC7	SOFTWARE	ASN A:146 , ASN A:282 , ALA A:283 , HOH A:440 , HOH A:622 , HOH A:717	BINDING SITE FOR RESIDUE GOL A 11
08	AC8	SOFTWARE	ASP A:360	BINDING SITE FOR RESIDUE AZI A 379
09	AC9	SOFTWARE	ARG A:290 , PRO A:312 , PRO A:316 , ASP A:318	BINDING SITE FOR RESIDUE GOL A 380
10	BC1	SOFTWARE	TYR A:187 , ASP A:249	BINDING SITE FOR RESIDUE GOL A 381
11	BC2	SOFTWARE	ILE A:108 , LYS A:109 , ALA A:111 , LYS A:112 , THR A:363 , GLN A:376 , HOH A:505 , HOH A:662 , HOH A:747	BINDING SITE FOR RESIDUE GOL A 382
12	BC3	SOFTWARE	GLY A:123 , SER A:124 , ASP A:125 , GLU A:141 , ILE A:367 , TYR A:377 , HOH A:586	BINDING SITE FOR RESIDUE GOL A 383
13	BC4	SOFTWARE	GLY A:200 , ARG A:201 , GOL A:387	BINDING SITE FOR RESIDUE GOL A 384
14	BC5	SOFTWARE	LEU A:161 , ASN A:164 , GLY A:303 , GLY A:304 , ASN A:326 , HOH A:596	BINDING SITE FOR RESIDUE AZI A 385
15	BC6	SOFTWARE	GOL A:9 , LYS A:349 , HOH A:435	BINDING SITE FOR RESIDUE GOL A 386
16	BC7	SOFTWARE	THR A:104 , ALA A:105 , GLU A:106 , ASP A:128 , GLY A:200 , ASP A:221 , GOL A:384 , HOH A:434 , HOH A:742	BINDING SITE FOR RESIDUE GOL A 387

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	D_2_HYDROXYACID_DH_1	PS00065	D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.	FDH_ARATH	200-227	1	A:194-221
2	D_2_HYDROXYACID_DH_2	PS00670	D-isomer specific 2-hydroxyacid dehydrogenases signature 2.	FDH_ARATH	250-272	1	A:244-266
3	D_2_HYDROXYACID_DH_3	PS00671	D-isomer specific 2-hydroxyacid dehydrogenases signature 3.	FDH_ARATH	279-295	1	A:273-289

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	D_2_HYDROXYACID_DH_1	PS00065	D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.	FDH_ARATH	200-227	1	A:194-221
2	D_2_HYDROXYACID_DH_2	PS00670	D-isomer specific 2-hydroxyacid dehydrogenases signature 2.	FDH_ARATH	250-272	1	A:244-266
3	D_2_HYDROXYACID_DH_3	PS00671	D-isomer specific 2-hydroxyacid dehydrogenases signature 3.	FDH_ARATH	279-295	1	A:273-289

Biological Unit 2 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	D_2_HYDROXYACID_DH_1	PS00065	D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.	FDH_ARATH	200-227	2	A:194-221
2	D_2_HYDROXYACID_DH_2	PS00670	D-isomer specific 2-hydroxyacid dehydrogenases signature 2.	FDH_ARATH	250-272	2	A:244-266
3	D_2_HYDROXYACID_DH_3	PS00671	D-isomer specific 2-hydroxyacid dehydrogenases signature 3.	FDH_ARATH	279-295	2	A:273-289

Exons (0, 0)

Sequences/Alignments

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
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Chain A from PDB  Type:PROTEIN  Length:351
 aligned with FDH_ARATH | Q9S7E4 from UniProtKB/Swiss-Prot  Length:384

    Alignment length:351
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383 
            FDH_ARATH    34 DSKKIVGVFYKANEYATKNPNFLGCVENALGIRDWLESQGHQYIVTDDKEGPDCELEKHIPDLHVLISTPFHPAYVTAERIKKAKNLKLLLTAGIGSDHIDLQAAAAAGLTVAEVTGSNVVSVAEDELMRILILMRNFVPGYNQVVKGEWNVAGIAYRAYDLEGKTIGTVGAGRIGKLLLQRLKPFGCNLLYHDRLQMAPELEKETGAKFVEDLNEMLPKCDVIVINMPLTEKTRGMFNKELIGKLKKGVLIVNNARGAIMERQAVVDAVESGHIGGYSGDVWDPQPAPKDHPWRYMPNQAMTPHTSGTTIDAQLRYAAGTKDMLERYFKGEDFPTENYIVKDGELAPQYR 384
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------2-Hacid_dh-3jtmA01 A:56-365                                                                                                                                                                                                                                                                                           ------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------2-Hacid_dh_C-3jtmA02 A:155-334                                                                                                                                                      -------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeee....hhhhhhh........hhhhhhhhhhhh..eeeee.......hhhhhhh....eeee........hhhhhhhh....eeee........hhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh........eeeee..hhhhhhhhhhhhhhh.eeeee.....hhhhhhhhh.ee..hhhhhhhhh.eeee............hhhhhhhh....eeee..hhhhhhhhhhhhhhhhh...eeee...........hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh...hhh.eeee..ee.hhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_1        ----------------------D_2_HYDROXYACID_DH_2   ------D_2_HYDROXYACID_D----------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jtm A  28 DSKKIVGVFYKANEYATKNPNFLGCVENALGIRDWLESQGHQYIVTDDKEGPDCELEKHIPDLHVLISTPFHPAYVTAERIKKAKNLKLLLTAGIGSDHIDLQAAAAAGLTVAEVTGSNVVSVAEDELMRILILMRNFVPGYNQVVKGEWNVAGIAYRAYDLEGKTIGTVGAGRIGKLLLQRLKPFGCNLLYHDRLQMAPELEKETGAKFVEDLNEMLPKCDVIVINMPLTEKTRGMFNKELIGKLKKGVLIVNNARGAIMERQAVVDAVESGHIGGYSGDVWDPQPAPKDHPWRYMPNQAMTPHTSGTTIDAQLRYAAGTKDMLERYFKGEDFPTENYIVKDGELAPQYR 378
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (2, 2)

Gene Ontology (14, 14)

Asymmetric Unit(hide GO term definitions)

Chain A (FDH_ARATH | Q9S7E4)

molecular function
	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:0008863	formate dehydrogenase (NAD+) activity	Catalysis of the reaction: formate + NAD(+) = CO(2) + NADH.
	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.
	GO:0004617	phosphoglycerate dehydrogenase activity	Catalysis of the reaction: 3-phosphoglycerate + NAD+ = 3-phosphohydroxypyruvate + NADH + H+.
biological process
	GO:0042183	formate catabolic process	The chemical reactions and pathways resulting in the breakdown of formate, also known as methanoate, the anion HCOO- derived from methanoic (formic) acid.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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:0046686	response to cadmium ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cadmium (Cd) ion stimulus.
	GO:0009070	serine family amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids of the serine family, comprising cysteine, glycine, homoserine, selenocysteine and serine.
cellular component
	GO:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
	GO:0009579	thylakoid	A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.

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		Asp A:311 - Pro A:312	[ RasMol ]
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	3jtm
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 16)

Sites (16, 16)