Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURES OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE COMPLEXES WITH NAD
 
Authors :  Y. C. Tien, P. Chuankhayan, Y. H. Lin, S. L. Chang, C. J. Chen
Date :  10 Dec 11  (Deposition) - 28 Nov 12  (Release) - 28 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym./Biol. Unit :  A,B,C,O
Keywords :  Rossmann Fold, Glyceraldehyde-3-Phosphate Dehydrogenase (Nad+) (Phosphorylating) Activity, Nad(H) Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. C. Tien, P. Chuankhayan, Y. C. Huang, C. D. Chen, J. Alikhajeh, S. L. Chang, C. J. Chen
Crystal Structures Of Rice (Oryza Sativa) Glyceraldehyde-3-Phosphate Dehydrogenase Complexes With Nad And Sulfate Suggest Involvement Of Phe37 In Nad Binding For Catalysis
Plant Mol. Biol. V. 80 389 2012
PubMed-ID: 22903596  |  Reference-DOI: 10.1007/S11103-012-9953-7

(-) Compounds

Molecule 1 - GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, CYTOSOLIC
    Chains: O, A, B, C
    EC Number: 1.2.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-SUMO
    Expression System Strain: BL21DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GAPC, GPC, OS08G0126300, LOC_OS08G03290, OJ1163_G08.15, OSJ_024858
    Organism Common: JAPANESE RICE
    Organism Scientific: ORYZA SATIVA JAPONICA GROUP
    Organism Taxid: 39947
    Synonym: PP38

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCO

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN O:9 , GLY O:10 , PHE O:11 , GLY O:12 , ARG O:13 , ILE O:14 , ASN O:34 , ASP O:35 , PRO O:36 , PHE O:37 , ARG O:82 , SER O:100 , THR O:101 , GLY O:102 , PHE O:104 , SER O:124 , ALA O:125 , CYS O:154 , ALA O:185 , ASN O:318 , TYR O:322 , HOH O:503 , HOH O:511 , HOH O:526 , HOH O:537 , HOH O:567 , HOH O:574 , HOH O:579 , HOH O:584BINDING SITE FOR RESIDUE NAD O 401
2AC2SOFTWAREASN A:9 , GLY A:10 , PHE A:11 , GLY A:12 , ARG A:13 , ILE A:14 , ASN A:34 , ASP A:35 , PRO A:36 , PHE A:37 , ARG A:82 , SER A:100 , THR A:101 , GLY A:102 , PHE A:104 , SER A:124 , ALA A:125 , CYS A:154 , ALA A:185 , ASN A:318 , TYR A:322 , HOH A:509 , HOH A:525 , HOH A:538 , HOH A:553 , HOH A:561 , HOH A:570BINDING SITE FOR RESIDUE NAD A 401
3AC3SOFTWAREASN B:9 , GLY B:10 , PHE B:11 , GLY B:12 , ARG B:13 , ILE B:14 , ASN B:34 , ASP B:35 , PRO B:36 , PHE B:37 , ARG B:82 , SER B:100 , THR B:101 , GLY B:102 , PHE B:104 , SER B:124 , ALA B:125 , CYS B:154 , ALA B:185 , ASN B:318 , TYR B:322 , HOH B:501 , HOH B:515 , HOH B:529 , HOH B:542 , HOH B:543 , HOH B:569 , HOH B:570 , HOH B:571 , HOH B:575 , HOH B:577 , HOH O:538BINDING SITE FOR RESIDUE NAD B 401
4AC4SOFTWAREHOH A:527 , ASN C:9 , GLY C:10 , PHE C:11 , GLY C:12 , ARG C:13 , ILE C:14 , ASP C:35 , PRO C:36 , PHE C:37 , ARG C:82 , SER C:100 , THR C:101 , GLY C:102 , PHE C:104 , SER C:124 , ALA C:125 , CYS C:154 , ALA C:185 , ASN C:318 , TYR C:322 , HOH C:507 , HOH C:516 , HOH C:521 , HOH C:536 , HOH C:551 , HOH C:564 , HOH C:574 , HOH C:576BINDING SITE FOR RESIDUE NAD C 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V1Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3V1Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V1Y)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAPDHPS00071 Glyceraldehyde 3-phosphate dehydrogenase active site.G3PC1_ORYSJ152-159
 
 
 		  4A:152-159
B:152-159
C:152-159
O:152-159

(-) Exons   (0, 0)

(no "Exon" information available for 3V1Y)

(-) Sequences/Alignments

Asymmetric/Biological 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:335
 aligned with G3PC1_ORYSJ | Q0J8A4 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:335
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332     
          G3PC1_ORYSJ     3 KIKIGINGFGRIGRLVARVALQSEDVELVAVNDPFITTDYMTYMFKYDTVHGQWKHSDIKIKDSKTLLLGEKPVTVFGIRNPDEIPWAEAGAEYVVESTGVFTDKEKAAAHLKGGAKKVVISAPSKDAPMFVCGVNEDKYTSDIDIVSNASCTTNCLAPLAKVIHDNFGIIEGLMTTVHAITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPDLNGKLTGMSFRVPTVDVSVVDLTVRIEKAASYDAIKSAIKSASEGKLKGIIGYVEEDLVSTDFVGDSRSSIFDAKAGIALNDNFVKLVAWYDNEWGYSNRVIDLIRHMAKTQ 337
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhh...........eeeee..eeee..eeeeee...hhhhhhhhhhh..eeee......hhhhhhhhhh....eeee..............hhhhh.....eee..hhhhhhhhhhhhhhhhhhheeeeeeeeee................hhhhhhhhhh.eeee.hhhhhhhhhhhhhh..eeeeeee......eeeeeeeee....hhhhhhhhhhhhhhh.....eeee....hhhhhh.....eeee....eeee..eeeeeeee..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v1y A   3 KIKIGINGFGRIGRLVARVALQSEDVELVAVNDPFITTDYMTYMFKYDTVHGQWKHSDIKIKDSKTLLLGEKPVTVFGIRNPDEIPWAEAGAEYVVESTGVFTDKEKAAAHLKGGAKKVVISAPSKDAPMFVCGVNEDKYTSDIDIVSNASCTTNCLAPLAKVIHDNFGIIEGLMTTVHAITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPDLNGKLTGMSFRVPTVDVSVVDLTVRIEKAASYDAIKSAIKSASEGKLKGIIGYVEEDLVSTDFVGDSRSSIFDAKAGIALNDNFVKLVAWYDNEWGYSNRVIDLIRHMAKTQ 337
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332     


Chain B from PDB  Type:PROTEIN  Length:336
 aligned with G3PC1_ORYSJ | Q0J8A4 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:336
                                    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      
          G3PC1_ORYSJ     2 GKIKIGINGFGRIGRLVARVALQSEDVELVAVNDPFITTDYMTYMFKYDTVHGQWKHSDIKIKDSKTLLLGEKPVTVFGIRNPDEIPWAEAGAEYVVESTGVFTDKEKAAAHLKGGAKKVVISAPSKDAPMFVCGVNEDKYTSDIDIVSNASCTTNCLAPLAKVIHDNFGIIEGLMTTVHAITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPDLNGKLTGMSFRVPTVDVSVVDLTVRIEKAASYDAIKSAIKSASEGKLKGIIGYVEEDLVSTDFVGDSRSSIFDAKAGIALNDNFVKLVAWYDNEWGYSNRVIDLIRHMAKTQ 337
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhh...........eeeee..eeee..eeeeee...hhhhhhhhhhh..eeee......hhhhhhhhhhhh..eeee..............hhhhh.....eee..hhhhhhhhhhhhhhhhhhheeeeeeeeee................hhhhhhhhhh.eeee.....hhhhhhhhhh..eeeeeee......eeeeeeeee....hhhhhhhhhhhhhhh.....eeee....hhhhhh.....eeee....eeee..eeeeeeee..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3v1y B   2 GKIKIGINGFGRIGRLVARVALQSEDVELVAVNDPFITTDYMTYMFKYDTVHGQWKHSDIKIKDSKTLLLGEKPVTVFGIRNPDEIPWAEAGAEYVVESTGVFTDKEKAAAHLKGGAKKVVISAPSKDAPMFVCGVNEDKYTSDIDIVSNASCTTNCLAPLAKVIHDNFGIIEGLMTTVHAITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPDLNGKLTGMSFRVPTVDVSVVDLTVRIEKAASYDAIKSAIKSASEGKLKGIIGYVEEDLVSTDFVGDSRSSIFDAKAGIALNDNFVKLVAWYDNEWGYSNRVIDLIRHMAKTQ 337
                                    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      


Chain C from PDB  Type:PROTEIN  Length:336
 aligned with G3PC1_ORYSJ | Q0J8A4 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:336
                                    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      
          G3PC1_ORYSJ     2 GKIKIGINGFGRIGRLVARVALQSEDVELVAVNDPFITTDYMTYMFKYDTVHGQWKHSDIKIKDSKTLLLGEKPVTVFGIRNPDEIPWAEAGAEYVVESTGVFTDKEKAAAHLKGGAKKVVISAPSKDAPMFVCGVNEDKYTSDIDIVSNASCTTNCLAPLAKVIHDNFGIIEGLMTTVHAITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPDLNGKLTGMSFRVPTVDVSVVDLTVRIEKAASYDAIKSAIKSASEGKLKGIIGYVEEDLVSTDFVGDSRSSIFDAKAGIALNDNFVKLVAWYDNEWGYSNRVIDLIRHMAKTQ 337
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhh...........eeeee..eeee..eeeeee...hhhhhhhhhhh..eeee......hhhhhhhhhhh...eeee..............hhhhh.....eee..hhhhhhhhhhhhhhhhhhheeeeeeeeee................hhhhhhhhhh.eee......hhhhhhhhhh..eeeeeee......eeeeeeeee....hhhhhhhhhhhhhh......eeee....hhhhhh.....eeee....eeee..eeeeeeee..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3v1y C   2 GKIKIGINGFGRIGRLVARVALQSEDVELVAVNDPFITTDYMTYMFKYDTVHGQWKHSDIKIKDSKTLLLGEKPVTVFGIRNPDEIPWAEAGAEYVVESTGVFTDKEKAAAHLKGGAKKVVISAPSKDAPMFVCGVNEDKYTSDIDIVSNASCTTNCLAPLAKVIHDNFGIIEGLMTTVHAITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPDLNGKLTGMSFRVPTVDVSVVDLTVRIEKAASYDAIKSAIKSASEGKLKGIIGYVEEDLVSTDFVGDSRSSIFDAKAGIALNDNFVKLVAWYDNEWGYSNRVIDLIRHMAKTQ 337
                                    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      


Chain O from PDB  Type:PROTEIN  Length:336
 aligned with G3PC1_ORYSJ | Q0J8A4 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:336
                                    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      
          G3PC1_ORYSJ     2 GKIKIGINGFGRIGRLVARVALQSEDVELVAVNDPFITTDYMTYMFKYDTVHGQWKHSDIKIKDSKTLLLGEKPVTVFGIRNPDEIPWAEAGAEYVVESTGVFTDKEKAAAHLKGGAKKVVISAPSKDAPMFVCGVNEDKYTSDIDIVSNASCTTNCLAPLAKVIHDNFGIIEGLMTTVHAITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPDLNGKLTGMSFRVPTVDVSVVDLTVRIEKAASYDAIKSAIKSASEGKLKGIIGYVEEDLVSTDFVGDSRSSIFDAKAGIALNDNFVKLVAWYDNEWGYSNRVIDLIRHMAKTQ 337
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhh...........eeeee..eeee..eeeeee...hhhhhhhhhhh..eeee......hhhhhhhhhhh...eeee..............hhhhh.....eee..hhhhhhhhhhhhhhhhhhheeeeeeeeee...............hhhhhhhhhhh.eeee.hhhhhhhhhhhhhh..eeeeeee......eeeeeeeee....hhhhhhhhhhhhhhh.....eeee....hhhhhh.....eeee....eeee..eeeeeeee..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3v1y O   2 GKIKIGINGFGRIGRLVARVALQSEDVELVAVNDPFITTDYMTYMFKYDTVHGQWKHSDIKIKDSKTLLLGEKPVTVFGIRNPDEIPWAEAGAEYVVESTGVFTDKEKAAAHLKGGAKKVVISAPSKDAPMFVCGVNEDKYTSDIDIVSNASCTTNCLAPLAKVIHDNFGIIEGLMTTVHAITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPDLNGKLTGMSFRVPTVDVSVVDLTVRIEKAASYDAIKSAIKSASEGKLKGIIGYVEEDLVSTDFVGDSRSSIFDAKAGIALNDNFVKLVAWYDNEWGYSNRVIDLIRHMAKTQ 337
                                    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
   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)

(no "SCOP Domain" information available for 3V1Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V1Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V1Y)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,O   (G3PC1_ORYSJ | Q0J8A4)
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:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0004365    glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity    Catalysis of the reaction: D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + NADH + H+.
    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:0016620    oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
biological process
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    NAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3v1y)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3v1y
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  G3PC1_ORYSJ | Q0J8A4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.2.1.12
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  G3PC1_ORYSJ | Q0J8A4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        G3PC1_ORYSJ | Q0J8A4: 3e5r 3e6a

(-) Related Entries Specified in the PDB File

3e5r CRYSTAL STRUCTURE OF NATIVE GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (GAPDH) FROM ORYZA SATIVA
3e6a CRYSTAL STRUCTURE OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM ORYZA SATIVA SOAKING WITH SULPHATE