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(-) Description

Title :  CRYSTAL STRUCTURE OF CANDIDA BOIDINII FORMATE DEHYDROGENASE COMPLEXED WITH NAD+ AND AZIDE
 
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 :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transition State, Ternary Complex, 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 - FDH
    Chains: A, B
    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

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1AZI2Ligand/IonAZIDE ION
2CL2Ligand/IonCHLORIDE ION
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:69 , VAL A:93 , ASN A:119 , VAL A:120 , VAL A:123 , GLY A:171 , GLY A:173 , ARG A:174 , ILE A:175 , TYR A:194 , ASP A:195 , TYR A:196 , ALA A:229 , PRO A:230 , HIS A:232 , THR A:235 , THR A:256 , ALA A:257 , ARG A:258 , ASP A:282 , VAL A:283 , HIS A:311 , SER A:313 , GLY A:314 , ALA A:357 , AZI A:502 , CL A:503 , HOH A:668 , HOH A:671 , HOH A:688 , HOH A:702 , HOH A:713 , HOH A:735 , HOH A:752 , HOH A:799 , HOH A:866 , HOH A:932binding site for residue NAD A 501
2AC2SOFTWAREPRO A:68 , PHE A:69 , GLY A:92 , VAL A:93 , ASN A:119 , ARG A:258 , HIS A:311 , NAD A:501binding site for residue AZI A 502
3AC3SOFTWAREHIS A:232 , NAD A:501 , HOH A:1016 , HOH A:1058binding site for residue CL A 503
4AC4SOFTWAREPHE B:69 , VAL B:93 , ASN B:119 , VAL B:120 , VAL B:123 , GLY B:171 , GLY B:173 , ARG B:174 , ILE B:175 , TYR B:194 , ASP B:195 , TYR B:196 , ALA B:229 , PRO B:230 , HIS B:232 , THR B:235 , THR B:256 , ALA B:257 , ARG B:258 , ASP B:282 , VAL B:283 , HIS B:311 , SER B:313 , GLY B:314 , ALA B:357 , AZI B:502 , CL B:503 , HOH B:675 , HOH B:684 , HOH B:685 , HOH B:690 , HOH B:706 , HOH B:759 , HOH B:772 , HOH B:789 , HOH B:874 , HOH B:950binding site for residue NAD B 501
5AC5SOFTWAREPRO B:68 , PHE B:69 , GLY B:92 , VAL B:93 , ASN B:119 , ARG B:258 , HIS B:311 , NAD B:501binding site for residue AZI B 502
6AC6SOFTWAREHIS B:232 , NAD B:501 , HOH B:1032binding site for residue CL B 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DN9)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological 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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DN9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DN9)

(-) Exons   (0, 0)

(no "Exon" information available for 5DN9)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhh........hhhhhhhhhhhh..eeeee.......hhhhhhhhhh.eeee........hhhhhhhh....eeee........hhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh........eeeee..hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhheee..hhhhhhhh..eeee............hhhhhh.....eeeee..hhhhhhhhhhhhhhhh..eeeeee........................eee...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhh.eeee..ee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dn9 A   1 MKIVLVLYDAGKHAADEEKLYGCTENKLGIANWLKDQGHELITTSDKEGGNSVLDQHIPDADIIITTPFHPAYITKERIDKAKKLKLVVVAGVGSDHIDLDYINQTGKKISVLEVTGSNVVSVAEHVLMTMLVLVRNFVPAHEQIINHDWEVAAIAKDAYDIEGKTIATIGAGRIGYRVLERLVPFNPKELLYYDYQALPKDAEEKVGARRVENIEELVAQADIVTINAPLHAGTKGLINKELLSKFKKGAWLVNTARGAICVAEDVAAALESGQLRGYGGDVWFPQPAPKDHPWRDMRNKYGAGNAMTPHYSGTTLDAQTRYAEGTKNILESFFTGKFDYRPQDIILLNGEYITKAYGKH 361
                                    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       360 


Chain B from PDB  Type:PROTEIN  Length:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhh........hhhhhhhhhhhh..eeeee.......hhhhhhhhhh.eeee........hhhhhhhh....eeee........hhhhhhhh....eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh........eeeee..hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhheee..hhhhhhhh..eeee............hhhhhh.....eeeee..hhhhhhhhhhhhhhhh..eeeeee...........hhhhhh.......eee...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhh.eeee..ee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dn9 B   1 MKIVLVLYDAGKHAADEEKLYGCTENKLGIANWLKDQGHELITTSDKEGGNSVLDQHIPDADIIITTPFHPAYITKERIDKAKKLKLVVVAGVGSDHIDLDYINQTGKKISVLEVTGSNVVSVAEHVLMTMLVLVRNFVPAHEQIINHDWEVAAIAKDAYDIEGKTIATIGAGRIGYRVLERLVPFNPKELLYYDYQALPKDAEEKVGARRVENIEELVAQADIVTINAPLHAGTKGLINKELLSKFKKGAWLVNTARGAICVAEDVAAALESGQLRGYGGDVWFPQPAPKDHPWRDMRNKYGAGNAMTPHYSGTTLDAQTRYAEGTKNILESFFTGKFDYRPQDIILLNGEYITKAYGKH 361
                                    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       360
   Legend:   → Mismatch (orange background)
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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 5DN9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DN9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DN9)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5DN9)

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  Cis Peptide Bonds
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        A0A0A1EQY0_C | A0A0A1EQY0: 5dna

(-) Related Entries Specified in the PDB File

5dn4 5dn5 5dna