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(-) Description

Title :  CRYSTAL STRUCTURE OF A BACTERIAL DEHYDROGENASE AT 2.19 ANGSTROMS RESOLUTION
 
Authors :  J. Querol-Garcia, F. J. Fernandez, S. Gomez, D. Fulla, J. Juanhuix, M. C
Date :  23 Jun 16  (Deposition) - 12 Jul 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Atopobium Vaginae, Gapdh, Nad, Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Querol-Garcia, F. J. Fernandez, A. V. Marin, S. Gomez, D. Fulla, C. Melchor-Tafur, V. Franco-Hidalgo, S. Alberti, J. Juanhuix, S. Rodriguez De Cordoba, J. R. Regueiro, M. C. Vega
Crystal Structure Of Glyceraldehyde-3-Phosphate Dehydrogenase From The Gram-Positive Bacterial Pathogen A. Vaginae, An Immunoevasive Factor That Interacts With The Human C5A Anaphylatoxin.
Front Microbiol V. 8 541 2017
PubMed-ID: 28443070  |  Reference-DOI: 10.3389/FMICB.2017.00541

(-) Compounds

Molecule 1 - GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21B
    Expression System Taxid: 469008
    Expression System Variant: ROSSETTA PLYSS
    Expression System Vector Type: PLASMID
    Gene: GAP, HMPREF0091_11005
    Organism Scientific: ATOPOBIUM VAGINAE
    Organism Taxid: 525256

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric/Biological Unit (2, 16)
No.NameCountTypeFull Name
1GOL12Ligand/IonGLYCEROL
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:24 , GLY A:26 , ARG A:27 , ILE A:28 , ASP A:49 , LEU A:50 , ALA A:95 , CYS A:113 , THR A:114 , GLY A:115 , PHE A:116 , SER A:137 , ALA A:138 , ASN A:336 , TYR A:340 , HOH A:508 , HOH A:517 , HOH A:529 , HOH A:538 , HOH A:544 , HOH A:547 , PRO B:207 , HOH B:520binding site for residue NAD A 401
02AC2SOFTWAREASN A:68 , ARG A:71 , HOH A:513 , ASP D:301 , TYR D:307 , HOH D:536binding site for residue GOL A 402
03AC3SOFTWAREASN A:68 , TYR A:69 , ASN A:72binding site for residue GOL A 403
04AC4SOFTWAREPRO A:139 , SER A:167 , THR A:228 , GLY A:229 , ALA A:230 , HOH A:501binding site for residue GOL A 404
05AC5SOFTWAREALA A:220 , PRO A:253 , PRO B:253 , ALA C:220 , ALA D:220binding site for residue GOL A 405
06AC6SOFTWAREPRO A:207 , HOH A:510 , GLY B:24 , GLY B:26 , ARG B:27 , ILE B:28 , ASP B:49 , LEU B:50 , ALA B:95 , CYS B:113 , THR B:114 , GLY B:115 , SER B:137 , ALA B:138 , CYS B:168 , ASN B:336 , TYR B:340 , HOH B:509 , HOH B:511 , HOH B:526 , HOH B:528 , HOH B:543binding site for residue NAD B 401
07AC7SOFTWAREASP B:301 , MET B:305 , TYR B:307 , ASN C:68 , ARG C:71binding site for residue GOL B 402
08AC8SOFTWARETHR B:314 , ARG D:214 , ASN D:226binding site for residue GOL B 403
09AC9SOFTWAREASN B:150 , VAL B:151 , HIS B:153 , GLU B:154binding site for residue GOL B 404
10AD1SOFTWARETYR B:62 , ASN B:68 , ARG B:71 , ASP C:301binding site for residue GOL B 405
11AD2SOFTWAREARG B:214 , HOH B:544 , THR D:314binding site for residue GOL B 406
12AD3SOFTWAREGLY C:24 , GLY C:26 , ARG C:27 , ILE C:28 , ASN C:48 , ASP C:49 , LEU C:50 , ALA C:95 , CYS C:113 , THR C:114 , GLY C:115 , PHE C:116 , SER C:137 , ALA C:138 , ASN C:336 , TYR C:340 , HOH C:511 , HOH C:516 , HOH C:530 , HOH C:532 , HOH C:540 , HOH C:546 , HOH C:549 , HOH C:551 , PRO D:207binding site for residue NAD C 401
13AD4SOFTWARETHR A:314 , HOH A:553 , ARG C:214 , ASN C:226binding site for residue GOL C 402
14AD5SOFTWAREVAL C:274 , ASN C:278 , ALA C:313 , THR C:314 , THR C:316binding site for residue GOL C 403
15AD6SOFTWAREPRO C:207 , HOH C:536 , GLY D:24 , GLY D:26 , ARG D:27 , ILE D:28 , ASN D:48 , ASP D:49 , LEU D:50 , ALA D:95 , CYS D:113 , THR D:114 , GLY D:115 , PHE D:116 , SER D:137 , ALA D:138 , ASN D:336 , TYR D:340 , HOH D:515 , HOH D:517 , HOH D:531 , HOH D:535 , HOH D:538 , HOH D:541 , HOH D:547 , HOH D:548binding site for residue NAD D 401
16AD7SOFTWAREASN D:68 , ARG D:71binding site for residue GOL D 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LD5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LD5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LD5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LD5)

(-) Exons   (0, 0)

(no "Exon" information available for 5LD5)

(-) 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:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhh....eeeeeee...hhhhhhhhhhh.....hhhhh..eee...eeee..eeeeee...hhhhh........eeee......hhhhhhhhhhh...eeee...............hhhhh.....eee..hhhhhhhhhhhhhhhhhh.eeeeeeeeeee.....................hhhhh.eeee.....hhhhhhhhhh..eeeeeeee.....eeeeeeeeee.....hhhhhhhhhhhh.....eeee....hhhhhh.....eeee.hhheeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ld5 A  15 SMAVKVAINGFGRIGRLAFRQMFGHEGSEIVAINDLTDPKMLANLLKYDSSQGNYARNHSVVAGEDSITVDGKTIKIYKEADAHNLPWGELNVDVVLECTGFYTSKAKAQAHIDAGAKKVVISAPAGKDLPTIVYNVNHEILTKDDNIISAASCTTNCLAPMAKALNDFAPIQSGIMSTIHAFTGDQMVLDGPHRKGDLRRARAAAINIVPNSTGAAKAIGLVIPELNGKLIGSAQRVPVPTGSTTLLFAVVKSDKEITVDSINAAMKAASDPETFGYNEDPIVSSDIIGMTYGSLFDATQTMVQDLGNGLYQVEVVSWYDNENSYTSQMVRTIKYFEKFV 355
                                    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 


Chain B from PDB  Type:PROTEIN  Length:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhh....eeeeeee...hhhhhhhhhhh.....hhhhh..eee...eeee..eeeeee...hhhhh........eeee......hhhhhhhhhhh...eeee...............hhhhh.....eee..hhhhhhhhhhhhhhhhhh.eeeeeeeeeee...........................eeee.....hhhhhhhhhh..eeeeeeee.....eeeeeeeeee.....hhhhhhhhhhhhh....eeee....hhhhhh.....eeee.hhheeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ld5 B  16 MAVKVAINGFGRIGRLAFRQMFGHEGSEIVAINDLTDPKMLANLLKYDSSQGNYARNHSVVAGEDSITVDGKTIKIYKEADAHNLPWGELNVDVVLECTGFYTSKAKAQAHIDAGAKKVVISAPAGKDLPTIVYNVNHEILTKDDNIISAASCTTNCLAPMAKALNDFAPIQSGIMSTIHAFTGDQMVLDGPHRKGDLRRARAAAINIVPNSTGAAKAIGLVIPELNGKLIGSAQRVPVPTGSTTLLFAVVKSDKEITVDSINAAMKAASDPETFGYNEDPIVSSDIIGMTYGSLFDATQTMVQDLGNGLYQVEVVSWYDNENSYTSQMVRTIKYFEKFV 355
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355


Chain C from PDB  Type:PROTEIN  Length:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhh....eeeeeee...hhhhhhhhhhh.....hhhhh..eee...eeee..eeeeee...hhhhh........eeee......hhhhhhhhhhhh..eeee...............hhhhh.....eee..hhhhhhhhhhhhhhhhhh.eeeeeeeeeee.....................hhhhh.eeee.....hhhhhhhhhh..eeeeeeee.....eeeeeeeeee.....hhhhhhhhhhhh.....eeee....hhhhhh.....eeee.hhheeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ld5 C  15 SMAVKVAINGFGRIGRLAFRQMFGHEGSEIVAINDLTDPKMLANLLKYDSSQGNYARNHSVVAGEDSITVDGKTIKIYKEADAHNLPWGELNVDVVLECTGFYTSKAKAQAHIDAGAKKVVISAPAGKDLPTIVYNVNHEILTKDDNIISAASCTTNCLAPMAKALNDFAPIQSGIMSTIHAFTGDQMVLDGPHRKGDLRRARAAAINIVPNSTGAAKAIGLVIPELNGKLIGSAQRVPVPTGSTTLLFAVVKSDKEITVDSINAAMKAASDPETFGYNEDPIVSSDIIGMTYGSLFDATQTMVQDLGNGLYQVEVVSWYDNENSYTSQMVRTIKYFEKFVA 356
                                    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  


Chain D from PDB  Type:PROTEIN  Length:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhh....eeeeeee...hhhhhhhhhhh.....hhhhh..eee...eeee..eeeeee...hhhhh........eeee......hhhhhhhhhhh...eeee...............hhhhh.....eee..hhhhhhhhhhhhhhhhhh.eeeeeeeeeee.....................hhhhh.eeee.....hhhhhhhhhh..eeeeeeee.....eeeeeeeeee.....hhhhhhhhhhhh.....eeee....hhhhhh.....eeee.hhheeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ld5 D  16 MAVKVAINGFGRIGRLAFRQMFGHEGSEIVAINDLTDPKMLANLLKYDSSQGNYARNHSVVAGEDSITVDGKTIKIYKEADAHNLPWGELNVDVVLECTGFYTSKAKAQAHIDAGAKKVVISAPAGKDLPTIVYNVNHEILTKDDNIISAASCTTNCLAPMAKALNDFAPIQSGIMSTIHAFTGDQMVLDGPHRKGDLRRARAAAINIVPNSTGAAKAIGLVIPELNGKLIGSAQRVPVPTGSTTLLFAVVKSDKEITVDSINAAMKAASDPETFGYNEDPIVSSDIIGMTYGSLFDATQTMVQDLGNGLYQVEVVSWYDNENSYTSQMVRTIKYFEKFV 355
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355
   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

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(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LD5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LD5)

(-) Gene Ontology  (0, 0)

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