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(-) Description

Title :  CRYSTAL STRUCTURE OF CANDIDA BOIDINII FORMATE DEHYDROGENASE
 
Authors :  Q. Guo, L. Gakhar, K. Wichersham, K. Francis, A. Vardi-Kilshtain, D. T. C. M. Cheatum, A. Kohen
Date :  09 Sep 15  (Deposition) - 04 May 16  (Release) - 25 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Isozyme, Recombinant, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Guo, L. Gakhar, K. Wickersham, K. Francis, A. Vardi-Kilshtain, D. T. Major, C. M. Cheatum, A. Kohen
Structural And Kinetic Studies Of Formate Dehydrogenase Fro Candida Boidinii.
Biochemistry V. 55 2760 2016
PubMed-ID: 27100912  |  Reference-DOI: 10.1021/ACS.BIOCHEM.6B00181

(-) Compounds

Molecule 1 - FORMATE DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.2.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Taxid: 866768
    Gene: FDH
    Organism Common: YEAST
    Organism Scientific: CANDIDA BOIDINII
    Organism Taxid: 5477

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:197 , ALA A:198 , ARG A:211 , HOH A:514 , HOH A:524 , HOH A:613binding site for residue SO4 A 401
2AC2SOFTWAREGLY A:173 , ARG A:174 , HOH A:506 , HOH A:518 , HOH A:744binding site for residue SO4 A 402
3AC3SOFTWAREGLY B:173 , ARG B:174 , HOH B:547 , HOH B:730 , HOH B:774binding site for residue SO4 B 401
4AC4SOFTWAREGLY D:173 , ARG D:174 , HOH D:502 , HOH D:509 , HOH D:572 , HOH D:728binding site for residue SO4 D 401
5AC5SOFTWAREGLN D:197 , ALA D:198 , ARG D:211 , HOH D:503 , HOH D:632binding site for residue SO4 D 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DNA)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Phe A:285 -Pro A:286
2Gln A:287 -Pro A:288
3Phe B:285 -Pro B:286
4Gln B:287 -Pro B:288
5Phe C:285 -Pro C:286
6Gln C:287 -Pro C:288
7Phe D:285 -Pro D:286
8Gln D:287 -Pro D:288

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DNA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DNA)

(-) Exons   (0, 0)

(no "Exon" information available for 5DNA)

(-) 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:356
                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhh........hhhhhhhhhhhh..eeeee.......hhhhhhhhhh.eeee........hhhhhhhh....eeee........hhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh........eeeee..hhhhhhhhhhhhhhh..eeeee.....hhhhhhhh.eee..hhhhhhhh..eeee............hhhhhh.....eeeee..hhhhhhhhhhhhhhhh..eeeeee...........hhhhhh.......eee...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhh.eee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dna A   1 MKIVLVLYDAGKHAADEEKLYGCTENKLGIANWLKDQGHELITTSDKEGGNSVLDQHIPDADIIITTPFHPAYITKERIDKAKKLKLVVVAGVGSDHIDLDYINQTGKKISVLEVTGSNVVSVAEHVLMTMLVLVRNFVPAHEQIINHDWEVAAIAKDAYDIEGKTIATIGAGRIGYRVLERLVPFNPKELLYYDYQALPKDAEEKVGARRVENIEELVAQADIVTINAPLHAGTKGLINKELLSKFKKGAWLVNTARGAICVAEDVAAALESGQLRGYGGDVWFPQPAPKDHPWRDMRNKYGAGNAMTPHYSGTTLDAQTRYAEGTKNILESFFTGKFDYRPQDIILLNGEYITK 356
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350      


Chain B from PDB  Type:PROTEIN  Length:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhh........hhhhhhhhhhhh..eeeee.......hhhhhhhhhh.eeee........hhhhhhhh....eeee........hhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh........eeeee..hhhhhhhhhhhhhhh..eeeee.....hhhhhhhh.eee..hhhhhhhh..eeee............hhhhhh.....eeeee..hhhhhhhhhhhhhhhh..eeeeee...........hhhhhh.......eee...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhh.eee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dna B   1 MKIVLVLYDAGKHAADEEKLYGCTENKLGIANWLKDQGHELITTSDKEGGNSVLDQHIPDADIIITTPFHPAYITKERIDKAKKLKLVVVAGVGSDHIDLDYINQTGKKISVLEVTGSNVVSVAEHVLMTMLVLVRNFVPAHEQIINHDWEVAAIAKDAYDIEGKTIATIGAGRIGYRVLERLVPFNPKELLYYDYQALPKDAEEKVGARRVENIEELVAQADIVTINAPLHAGTKGLINKELLSKFKKGAWLVNTARGAICVAEDVAAALESGQLRGYGGDVWFPQPAPKDHPWRDMRNKYGAGNAMTPHYSGTTLDAQTRYAEGTKNILESFFTGKFDYRPQDIILLNGEY 353
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350   


Chain C from PDB  Type:PROTEIN  Length:350
                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhh.......hhhhhhhhhhh...eeeee.......hhhhhhhhhh.eeee........hhhhhhhh....eeee........hhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh........eeeee..hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhheee..hhhhhhhh..eeee............hhhhhh.....eeeee..hhhhhhhhhhhhhhhh..eeeeee...........hhhhhh.......eee...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhh.eee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dna C   1 MKIVLVLYDAGKHAKLYGCTENKLGIANWLKDQGHELITTSDKEGGNSVLDQHIPDADIIITTPFHPAYITKERIDKAKKLKLVVVAGVGSDHIDLDYINQTGKKISVLEVTGSNVVSVAEHVLMTMLVLVRNFVPAHEQIINHDWEVAAIAKDAYDIEGKTIATIGAGRIGYRVLERLVPFNPKELLYYDYQALPKDAEEKVGARRVENIEELVAQADIVTINAPLHAGTKGLINKELLSKFKKGAWLVNTARGAICVAEDVAAALESGQLRGYGGDVWFPQPAPKDHPWRDMRNKYGAGNAMTPHYSGTTLDAQTRYAEGTKNILESFFTGKFDYRPQDIILLNGEYI 354
                                    10   ||   24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354
                                        14|                                                                                                                                                                                                                                                                                                                                               
                                         19                                                                                                                                                                                                                                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:356
                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhh..........hhhhhhhhhhhh..eeeee.......hhhhhhhhhh.eeee........hhhhhhhh....eeee........hhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh........eeeee..hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhheee..hhhhhhhhh.eeee............hhhhhh.....eeeee..hhhhhhhhhhhhhhhhh.eeeeee...........hhhhhh.......eee...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhh.eee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dna D   1 MKIVLVLYDAGKHAADEEKLYGCTENKLGIANWLKDQGHELITTSDKEGGNSVLDQHIPDADIIITTPFHPAYITKERIDKAKKLKLVVVAGVGSDHIDLDYINQTGKKISVLEVTGSNVVSVAEHVLMTMLVLVRNFVPAHEQIINHDWEVAAIAKDAYDIEGKTIATIGAGRIGYRVLERLVPFNPKELLYYDYQALPKDAEEKVGARRVENIEELVAQADIVTINAPLHAGTKGLINKELLSKFKKGAWLVNTARGAICVAEDVAAALESGQLRGYGGDVWFPQPAPKDHPWRDMRNKYGAGNAMTPHYSGTTLDAQTRYAEGTKNILESFFTGKFDYRPQDIILLNGEYITK 356
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 5DNA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DNA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DNA)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5DNA)

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5dn9