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(-) Description

Title :  CRYSTAL STRUCTURE OF SERINE BOUND D-3-PHOSPHOGLYCERATE DEHYDROGENASE FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  S. Dey, J. C. Sacchettini
Date :  03 Jun 08  (Deposition) - 22 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
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
    Chains: A, B
    EC Number: 1.1.1.95
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SERA1
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: H37RV
    Synonym: PGDH

 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, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1SER2Mod. Amino AcidSERINE
2TLA3Ligand/IonL(+)-TARTARIC ACID
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1SER4Mod. Amino AcidSERINE
2TLA6Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:461 , ASP A:463 , ARG A:464 , PRO A:465 , GLY A:466 , ALA A:467 , LEU A:468 , LEU A:487 , ASN B:481 , ILE B:482BINDING SITE FOR RESIDUE SER A 600
2AC2SOFTWAREASN A:481 , ILE A:482 , TYR B:461 , ASP B:463 , ARG B:464 , GLY B:466 , LEU B:468 , LEU B:487BINDING SITE FOR RESIDUE SER B 600
3AC3SOFTWAREARG A:446 , HIS A:447 , HOH A:817 , LYS B:439 , ASP B:449 , LEU B:450 , ARG B:451 , ARG B:501BINDING SITE FOR RESIDUE TLA A 700
4AC4SOFTWARELYS 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:488BINDING SITE FOR RESIDUE TLA B 700
5AC5SOFTWAREGLU B:361 , GLU B:363 , LYS B:402BINDING SITE FOR RESIDUE TLA B 701

(-) SS Bonds  (1, 1)

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

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DC2)

(-) 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 3DC2)

(-) 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
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       528 
                                    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     | 
           SERA_MYCTO     3 LPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRLALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEEVEVLRLSALRGLFSAVIEDAVTFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGADGSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKIGTLLGTAGVNIQAAQLSEDAEGPGATILLRLDQDVPDDVRTAIAAAVDAYKLEVVDLS-   -
               SCOP domains d3dc2a1 A:4-98,A:283-316 Phosphoglycerate dehydrogenase                                        d3dc2a2 A:99-282 Phosphoglycerate dehydrogenase                                                                                                                                         d3dc2a1 A:4-98,A:283-316          d3dc2a3 A:317-451 D-3-phosphoglycerate dehydrogenase SerA                                                                              d3dc2a4 A:452-529                                                             - SCOP domains
               CATH domains 3dc2A01 A:4-98,A:281-320 NAD(P)-binding Rossmann-like Domain                                   3dc2A02 A:99-280 NAD(P)-binding Rossmann-like Domain                                                                                                                                  3dc2A01 A:4-98,A:281-320                3dc2A03 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.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh........eeeee..hhhhhhhhhhhhhh..eeeee....hhhhhhhh..ee.hhhhhhhhh.eeee............hhhhhh.....eeeee.......hhhhhhhhhhh..eeeeee..........hhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhh......eeeeeeee.hhhh.hhhhhhhhhhhhhhhhh.......hhhhhhhhhh.eeeeeee.......eeeeeeee.....eeeeeeeee....eeeeeee..eeeeee...eeeeeee....hhhhhhhhhhhhh...eeeeeee.......eeeeeee....hhhhhhhhhhhhh..eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_1        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACT  PDB: A:456-528 UniProt: 455-527                                     -- PROSITE (2)
                PROSITE (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_2   ------D_2_HYDROXYACID_D---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dc2 A   4 LPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRLALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEEVEVLRLSALRGLFSAVIEDAVTFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGADGSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKIGTLLGTAGVNIQAAQLSEDAEGPGATILLRLDQDVPDDVRTAIAAAVDAYKLEVVDLSS 600
                                    13        23        33        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       393       403       413       423       433       443       453       463       473       483       493       503       513       523     ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       529|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        600


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

    Alignment length:527
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       528 
                                    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     | 
           SERA_MYCTU     3 LPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRLALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEEVEVLRLSALRGLFSAVIEDAVTFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGADGSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKIGTLLGTAGVNIQAAQLSEDAEGPGATILLRLDQDVPDDVRTAIAAAVDAYKLEVVDLS-   -
               SCOP domains d3dc2a1 A:4-98,A:283-316 Phosphoglycerate dehydrogenase                                        d3dc2a2 A:99-282 Phosphoglycerate dehydrogenase                                                                                                                                         d3dc2a1 A:4-98,A:283-316          d3dc2a3 A:317-451 D-3-phosphoglycerate dehydrogenase SerA                                                                              d3dc2a4 A:452-529                                                             - SCOP domains
               CATH domains 3dc2A01 A:4-98,A:281-320 NAD(P)-binding Rossmann-like Domain                                   3dc2A02 A:99-280 NAD(P)-binding Rossmann-like Domain                                                                                                                                  3dc2A01 A:4-98,A:281-320                3dc2A03 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.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh........eeeee..hhhhhhhhhhhhhh..eeeee....hhhhhhhh..ee.hhhhhhhhh.eeee............hhhhhh.....eeeee.......hhhhhhhhhhh..eeeeee..........hhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhh......eeeeeeee.hhhh.hhhhhhhhhhhhhhhhh.......hhhhhhhhhh.eeeeeee.......eeeeeeee.....eeeeeeeee....eeeeeee..eeeeee...eeeeeee....hhhhhhhhhhhhh...eeeeeee.......eeeeeee....hhhhhhhhhhhhh..eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_1        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACT  PDB: A:456-528 UniProt: 455-527                                     -- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_2   ------D_2_HYDROXYACID_D---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dc2 A   4 LPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRLALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEEVEVLRLSALRGLFSAVIEDAVTFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGADGSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKIGTLLGTAGVNIQAAQLSEDAEGPGATILLRLDQDVPDDVRTAIAAAVDAYKLEVVDLSS 600
                                    13        23        33        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       393       403       413       423       433       443       453       463       473       483       493       503       513       523     ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       529|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        600


Chain B from PDB  Type:PROTEIN  Length:524
 aligned with SERA_MYCTO | P9WNX2 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:527
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       528 
                                    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     | 
           SERA_MYCTO     3 LPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRLALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEEVEVLRLSALRGLFSAVIEDAVTFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGADGSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKIGTLLGTAGVNIQAAQLSEDAEGPGATILLRLDQDVPDDVRTAIAAAVDAYKLEVVDLS-   -
               SCOP domains d3dc2b1 B:4-98,B:283-316 Phosphoglycerate dehydrogenase                                        d3dc2b2 B:99-282 Phosphoglycerate dehydrogenase                                                                                                                                         d3dc2b1 B:4-98,B:283-316          d3dc2b3 B:317-451 D-3-phosphoglycerate dehydrogenase SerA                                                                              d3dc2b4 B:452-529                                                             - SCOP domains
               CATH domains 3dc2B01 B:4-99,B:281-315 NAD(P)-binding Rossmann-like Domain                                    3dc2B02 B:100-280 NAD(P)-binding Rossmann-like Domain                                                                                                                                3dc2B01 B:4-99,B:281-315           3dc2B03 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............hhhhhh.....eeeee.......hhhhhhhhhhh..eeeeee..........hhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhhh.hhhhhhhhhhhhhhh...---..hhhhhhhhh...eeeeeee.......eeeeeeeee....eeeeeeeee....eeeeeee...eeeee...eeeeeeee...hhhhhhhhhhhhh...eeeeeeee.....eeeeeeee....hhhhhhhhhhhhh..eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_1        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACT  PDB: B:456-528 UniProt: 455-527                                     -- PROSITE (2)
                PROSITE (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_2   ------D_2_HYDROXYACID_D---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dc2 B   4 LPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRLALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEEVEVLRLSALRGLFSAVIE---TFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGADGSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKIGTLLGTAGVNIQAAQLSEDAEGPGATILLRLDQDVPDDVRTAIAAAVDAYKLEVVDLSS 600
                                    13        23        33        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       393       403       413       423       433       443       453       463       473       483       493       503       513       523     ||
                                                                                                                                                                                                                                                                                                                                                                                                                 379 383                                                                                                                                               529|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        600


Chain B from PDB  Type:PROTEIN  Length:524
 aligned with SERA_MYCTU | P9WNX3 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:527
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       528 
                                    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     | 
           SERA_MYCTU     3 LPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRLALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEEVEVLRLSALRGLFSAVIEDAVTFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGADGSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKIGTLLGTAGVNIQAAQLSEDAEGPGATILLRLDQDVPDDVRTAIAAAVDAYKLEVVDLS-   -
               SCOP domains d3dc2b1 B:4-98,B:283-316 Phosphoglycerate dehydrogenase                                        d3dc2b2 B:99-282 Phosphoglycerate dehydrogenase                                                                                                                                         d3dc2b1 B:4-98,B:283-316          d3dc2b3 B:317-451 D-3-phosphoglycerate dehydrogenase SerA                                                                              d3dc2b4 B:452-529                                                             - SCOP domains
               CATH domains 3dc2B01 B:4-99,B:281-315 NAD(P)-binding Rossmann-like Domain                                    3dc2B02 B:100-280 NAD(P)-binding Rossmann-like Domain                                                                                                                                3dc2B01 B:4-99,B:281-315           3dc2B03 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............hhhhhh.....eeeee.......hhhhhhhhhhh..eeeeee..........hhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhhh.hhhhhhhhhhhhhhh...---..hhhhhhhhh...eeeeeee.......eeeeeeeee....eeeeeeeee....eeeeeee...eeeee...eeeeeeee...hhhhhhhhhhhhh...eeeeeeee.....eeeeeeee....hhhhhhhhhhhhh..eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_1        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACT  PDB: B:456-528 UniProt: 455-527                                     -- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_2   ------D_2_HYDROXYACID_D---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dc2 B   4 LPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLAAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAALADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRLALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEEVEVLRLSALRGLFSAVIE---TFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGADGSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKIGTLLGTAGVNIQAAQLSEDAEGPGATILLRLDQDVPDDVRTAIAAAVDAYKLEVVDLSS 600
                                    13        23        33        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       393       403       413       423       433       443       453       463       473       483       493       503       513       523     ||
                                                                                                                                                                                                                                                                                                                                                                                                                 379 383                                                                                                                                               529|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        600
   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)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (4, 8)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DC2)

(-) Gene Ontology  (12, 21)

Asymmetric Unit(hide GO term definitions)
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.

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.

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  3dc2
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  1.1.1.95
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 Related Entries

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

UniProtKB/Swiss-Prot
        SERA_MYCTO | P9WNX2: 1ygy 3ddn
        SERA_MYCTU | P9WNX3: 1ygy 3ddn

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3DC2)