Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HYDROXYPYRUVIC ACID PHOSPHATE BOUND D-3-PHOSPHOGLYCERATE DEHYDROGENASE IN MYCOBACTERIUM TUBERCULOSIS
 
Authors :  S. Dey, J. C. Sacchettini
Date :  05 Jun 08  (Deposition) - 22 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Oxidoreductase, Phosphoglycerate Dehydrogenase, Serine Biosynthesis, Amino-Acid Biosynthesis, Nad (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Dey, R. L. Burton, G. A. Grant, J. C. Sacchettini
Structural Analysis Of Substrate And Effector Binding In Mycobacterium Tuberculosis D-3-Phosphoglycerate Dehydrogenase
Biochemistry V. 47 8271 2008
PubMed-ID: 18627175  |  Reference-DOI: 10.1021/BI800212B

(-) Compounds

Molecule 1 - D-3-PHOSPHOGLYCERATE DEHYDROGENASE
    ChainsA, B
    EC Number1.1.1.95
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET30B
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSERA1
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid1773
    StrainH37RV
    SynonymPGDH

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1HPV1Ligand/Ion2-OXO-3-(PHOSPHONOOXY)PROPANOIC ACID
2TLA3Ligand/IonL(+)-TARTARIC ACID
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1HPV2Ligand/Ion2-OXO-3-(PHOSPHONOOXY)PROPANOIC ACID
2TLA6Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:446 , HIS A:447 , HOH A:788 , LYS B:439 , ASP B:449 , LEU B:450 , ARG B:451 , ARG B:501BINDING SITE FOR RESIDUE TLA A 530
2AC2SOFTWARELYS A:439 , ASP A:449 , LEU A:450 , ARG A:451 , ALA A:484 , ARG A:501 , ARG B:446 , HIS B:447 , SER B:488 , GLU B:489BINDING SITE FOR RESIDUE TLA B 530
3AC3SOFTWAREGLU B:361 , GLU B:363 , LYS B:402BINDING SITE FOR RESIDUE TLA B 531
4AC4SOFTWAREARG A:132 , SER B:52 , ARG B:72 , GLY B:76 , ASN B:99 , ALA B:283 , GLN B:289 , HOH B:730BINDING SITE FOR RESIDUE HPV B 600

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:401 -B:401

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:262 -Pro A:263
2Pro B:208 -Glu B:209
3Glu B:262 -Pro B:263

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (4, 8)

Asymmetric Unit (4, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1D_2_HYDROXYACID_DH_1PS00065 D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.SERA_MYCTO144-171
 
  2A:145-172
B:145-172
SERA_MYCTU144-171
 
  2A:145-172
B:145-172
2D_2_HYDROXYACID_DH_2PS00670 D-isomer specific 2-hydroxyacid dehydrogenases signature 2.SERA_MYCTO192-214
 
  2A:193-215
B:193-215
SERA_MYCTU192-214
 
  2A:193-215
B:193-215
3D_2_HYDROXYACID_DH_3PS00671 D-isomer specific 2-hydroxyacid dehydrogenases signature 3.SERA_MYCTO221-237
 
  2A:222-238
B:222-238
SERA_MYCTU221-237
 
  2A:222-238
B:222-238
4ACTPS51671 ACT domain profile.SERA_MYCTO455-527
 
  2A:456-528
B:456-528
SERA_MYCTU455-527
 
  2A:456-528
B:456-528
Biological Unit 1 (4, 32)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1D_2_HYDROXYACID_DH_1PS00065 D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.SERA_MYCTO144-171
 
  4A:145-172
B:145-172
SERA_MYCTU144-171
 
  4A:145-172
B:145-172
2D_2_HYDROXYACID_DH_2PS00670 D-isomer specific 2-hydroxyacid dehydrogenases signature 2.SERA_MYCTO192-214
 
  4A:193-215
B:193-215
SERA_MYCTU192-214
 
  4A:193-215
B:193-215
3D_2_HYDROXYACID_DH_3PS00671 D-isomer specific 2-hydroxyacid dehydrogenases signature 3.SERA_MYCTO221-237
 
  4A:222-238
B:222-238
SERA_MYCTU221-237
 
  4A:222-238
B:222-238
4ACTPS51671 ACT domain profile.SERA_MYCTO455-527
 
  4A:456-528
B:456-528
SERA_MYCTU455-527
 
  4A:456-528
B:456-528

(-) Exons   (0, 0)

(no "Exon" information available for 3DDN)

(-) 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
(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:527
 aligned with SERA_MYCTO | P9WNX2 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:527
                                    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       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       
           SERA_MYCTO     2 SLPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRLALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEEVEVLRLSALRGLFSAVIEDAVTFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGADGSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKIGTLLGTAGVNIQAAQLSEDAEGPGATILLRLDQDVPDDVRTAIAAAVDAYKLEVVDLS 528
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ddnA01 A:3-98,A:281-320 NAD(P)-binding Rossmann-like Domain                                    3ddnA02 A:99-280 NAD(P)-binding Rossmann-like Domain                                                                                                                                  3ddnA01 A:3-98,A:281-320                3ddnA03 A:321-453 D-3-phosphoglycerate dehydrogenase; domain 3                                                                       ---------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....hhhhh......eeee....hhhhhhhhhhhh.eeee......hhhhhhhh....eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh........eeeee..hhhhhhhhhhhhh...eeeee....hhhhhhhh..ee.hhhhhhhhh.eeee............hhhhhh.....eeeee.......hhhhhhhhhhh..eeeeee..........hhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhh......eeeeeeee.hhhh.hhhhhhhhhhhhhhhhh.......hhhhhhhhhh.eeeeeee.......eeeeeeee.....eeeeeeeee....eeeeeee..eeeeee...eeeeeee....hhhhhhhhhhhhh...eeeeeeee......eeeeeee....hhhhhhhhhhhhheeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_1        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_2   ------D_2_HYDROXYACID_D-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACT  PDB: A:456-528 UniProt: 455-527                                     - PROSITE (1)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ddn A   3 SLPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRLALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEEVEVLRLSALRGLFSAVIEDAVTFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGADGSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKIGTLLGTAGVNIQAAQLSEDAEGPGATILLRLDQDVPDDVRTAIAAAVDAYKLEVVDLS 529
                                    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       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       

Chain A from PDB  Type:PROTEIN  Length:527
 aligned with SERA_MYCTU | P9WNX3 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:527
                                    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       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       
           SERA_MYCTU     2 SLPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRLALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEEVEVLRLSALRGLFSAVIEDAVTFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGADGSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKIGTLLGTAGVNIQAAQLSEDAEGPGATILLRLDQDVPDDVRTAIAAAVDAYKLEVVDLS 528
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ddnA01 A:3-98,A:281-320 NAD(P)-binding Rossmann-like Domain                                    3ddnA02 A:99-280 NAD(P)-binding Rossmann-like Domain                                                                                                                                  3ddnA01 A:3-98,A:281-320                3ddnA03 A:321-453 D-3-phosphoglycerate dehydrogenase; domain 3                                                                       ---------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....hhhhh......eeee....hhhhhhhhhhhh.eeee......hhhhhhhh....eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh........eeeee..hhhhhhhhhhhhh...eeeee....hhhhhhhh..ee.hhhhhhhhh.eeee............hhhhhh.....eeeee.......hhhhhhhhhhh..eeeeee..........hhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhh......eeeeeeee.hhhh.hhhhhhhhhhhhhhhhh.......hhhhhhhhhh.eeeeeee.......eeeeeeee.....eeeeeeeee....eeeeeee..eeeeee...eeeeeee....hhhhhhhhhhhhh...eeeeeeee......eeeeeee....hhhhhhhhhhhhheeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_1        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_2   ------D_2_HYDROXYACID_D-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACT  PDB: A:456-528 UniProt: 455-527                                     - PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ddn A   3 SLPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRLALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEEVEVLRLSALRGLFSAVIEDAVTFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGADGSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKIGTLLGTAGVNIQAAQLSEDAEGPGATILLRLDQDVPDDVRTAIAAAVDAYKLEVVDLS 529
                                    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       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       

Chain B from PDB  Type:PROTEIN  Length:525
 aligned with SERA_MYCTO | P9WNX2 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:527
                                    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       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       
           SERA_MYCTO     2 SLPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRLALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEEVEVLRLSALRGLFSAVIEDAVTFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGADGSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKIGTLLGTAGVNIQAAQLSEDAEGPGATILLRLDQDVPDDVRTAIAAAVDAYKLEVVDLS 528
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ddnB01 B:3-99,B:281-315 NAD(P)-binding Rossmann-like Domain                                     3ddnB02 B:100-280 NAD(P)-binding Rossmann-like Domain                                                                                                                                3ddnB01 B:3-99,B:281-315           3ddnB03 B:316-454 D-3-phosphoglycerate dehydrogenase; domain 3                                                                             --------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhh...eeee....hhhhhhhhhhhh.eeee......hhhhhhh.....eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh........eeeee..hhhhhhhhhhhhh...eeeee....hhhhhhhh.eee.hhhhhhhhh.eeee............hhhhhhhh....eeee.......hhhhhhhhhhh....eeee..........hhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhh....eeeeeeeeee.hhhh.hhhhhhhhhhhhhhh...--....hhhhhhhh...eeeeeee.......eeeeeeeee....eeeeeeeee....eeeeeee..eeeeee...eeeeeeee...hhhhhhhhhhhhh...eeeeeeee.....eeeeeeee....hhhhhhhhhhhhh..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_1        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_2   ------D_2_HYDROXYACID_D-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACT  PDB: B:456-528 UniProt: 455-527                                     - PROSITE (1)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ddn B   3 SLPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRLALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEEVEVLRLSALRGLFSAVIE--VTFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGADGSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKIGTLLGTAGVNIQAAQLSEDAEGPGATILLRLDQDVPDDVRTAIAAAVDAYKLEVVDLS 529
                                    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       342       352       362       372      |382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       
                                                                                                                                                                                                                                                                                                                                                                                                                  379  |                                                                                                                                                   
                                                                                                                                                                                                                                                                                                                                                                                                                     382                                                                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:525
 aligned with SERA_MYCTU | P9WNX3 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:527
                                    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       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       
           SERA_MYCTU     2 SLPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRLALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEEVEVLRLSALRGLFSAVIEDAVTFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGADGSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKIGTLLGTAGVNIQAAQLSEDAEGPGATILLRLDQDVPDDVRTAIAAAVDAYKLEVVDLS 528
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ddnB01 B:3-99,B:281-315 NAD(P)-binding Rossmann-like Domain                                     3ddnB02 B:100-280 NAD(P)-binding Rossmann-like Domain                                                                                                                                3ddnB01 B:3-99,B:281-315           3ddnB03 B:316-454 D-3-phosphoglycerate dehydrogenase; domain 3                                                                             --------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhh...eeee....hhhhhhhhhhhh.eeee......hhhhhhh.....eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh........eeeee..hhhhhhhhhhhhh...eeeee....hhhhhhhh.eee.hhhhhhhhh.eeee............hhhhhhhh....eeee.......hhhhhhhhhhh....eeee..........hhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhh....eeeeeeeeee.hhhh.hhhhhhhhhhhhhhh...--....hhhhhhhh...eeeeeee.......eeeeeeeee....eeeeeeeee....eeeeeee..eeeeee...eeeeeeee...hhhhhhhhhhhhh...eeeeeeee.....eeeeeeee....hhhhhhhhhhhhh..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_1        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_2   ------D_2_HYDROXYACID_D-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACT  PDB: B:456-528 UniProt: 455-527                                     - PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ddn B   3 SLPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRLALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEEVEVLRLSALRGLFSAVIE--VTFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGADGSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKIGTLLGTAGVNIQAAQLSEDAEGPGATILLRLDQDVPDDVRTAIAAAVDAYKLEVVDLS 529
                                    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       342       352       362       372      |382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       
                                                                                                                                                                                                                                                                                                                                                                                                                  379  |                                                                                                                                                   
                                                                                                                                                                                                                                                                                                                                                                                                                     382                                                                                                                                                   

   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 3DDN)

(-) CATH Domains  (2, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SERA_MYCTU | P9WNX3)
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:0016597    amino acid binding    Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
    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:0006564    L-serine biosynthetic process    The chemical reactions and pathways resulting in the formation of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    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.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    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.

Chain A,B   (SERA_MYCTO | P9WNX2)
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:0016597    amino acid binding    Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
    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:0006564    L-serine biosynthetic process    The chemical reactions and pathways resulting in the formation of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    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.

 Visualization

(-) Interactive Views

Asymmetric 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
    HPV  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TLA  [ 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
    Glu A:262 - Pro A:263   [ RasMol ]  
    Glu B:262 - Pro B:263   [ RasMol ]  
    Pro B:208 - Glu B:209   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3ddn
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SERA_MYCTO | P9WNX2
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  SERA_MYCTU | P9WNX3
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.1.1.95
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  SERA_MYCTO | P9WNX2
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SERA_MYCTU | P9WNX3
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SERA_MYCTO | P9WNX21ygy 3dc2
        SERA_MYCTU | P9WNX31ygy 3dc2

(-) Related Entries Specified in the PDB File

1ygy PGDH APOENZYME IN MYCOBACTERIUM TUBERCULOSIS
3dc2 SERINE BOUND PGDH IN MYCOBACTERIUM TUBERCULOSIS