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(-) Description

Title :  PDXS (G. STEAROTHERMOPHILUS) CO-CRYSTALLIZED WITH R5P
 
Authors :  J. L. Smith, A. M. Smith
Date :  14 Nov 14  (Deposition) - 14 Jan 15  (Release) - 11 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (2x)
Keywords :  Beta/Alpha Barrel, Pyridoxal 5-Phosphate, Glutamine Amidotransferase, Vitamin B6 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Smith, W. C. Brown, E. Harms, J. L. Smith
Crystal Structures Capture Three States In The Catalytic Cycle Of A Pyridoxal Phosphate (Plp) Synthase.
J. Biol. Chem. V. 290 5226 2015
PubMed-ID: 25568319  |  Reference-DOI: 10.1074/JBC.M114.626382

(-) Compounds

Molecule 1 - PYRIDOXAL BIOSYNTHESIS LYASE PDXS
    Chains: A, B, C, D, E, F
    EC Number: 4.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETTEV281
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PDXS, GK0011
    Organism Scientific: GEOBACILLUS KAUSTOPHILUS
    Organism Taxid: 235909
    Strain: HTA426

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (2x): ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1L5P6Mod. Amino Acid(2S)-2-AZANYL-6-[[(3R,4R)-3,4-BIS(OXIDANYL)-2-OXIDANYLIDENE-5-PHOSPHONOOXY-PENTYL]AMINO]HEXANOICACID
2LRK6Mod. Amino Acid(2S)-2-AZANYL-6-[[(2R,4R)-1,4-BIS(OXIDANYL)-3-OXIDANYLIDENE-5-PHOSPHONOOXY-PENTAN-2-YL]AMINO]HEXANOIC ACID
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1L5P12Mod. Amino Acid(2S)-2-AZANYL-6-[[(3R,4R)-3,4-BIS(OXIDANYL)-2-OXIDANYLIDENE-5-PHOSPHONOOXY-PENTYL]AMINO]HEXANOICACID
2LRK12Mod. Amino Acid(2S)-2-AZANYL-6-[[(2R,4R)-1,4-BIS(OXIDANYL)-3-OXIDANYLIDENE-5-PHOSPHONOOXY-PENTAN-2-YL]AMINO]HEXANOIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 4WXZ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WXZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4WXZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WXZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WXZ)

(-) Exons   (0, 0)

(no "Exon" information available for 4WXZ)

(-) 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:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhhhhhhhhhhh..eeee.........hhhhhhhhhhhh...eee.....hhhhhhhhhhh...eeee.............hhhhh...eeeee.hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhh....eee......hhhhhhhhhhh....eee.hhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wxz A  18 KGGVIMDVVNAEQAKIAEAAGAVAVMALERGVARMADPTVIEEVMNAVSIPVMAkVRIGHYVEARVLEALGVDYIDESEVLTPADEEFHIDKRQFTVPFVCGCRDLGEAARRIAEGASMLRTkGEPGTGNIVEAVRHMRKVNAQIRKVVNMSEDELVAEAKQLGAPVEVLREIKRLGRLPVVNFAAGGVTTPADAALMMHLGADGVFVGSGIFKSENPEKYARAIVEATTHYEDYELIAHLSKG 270
                                    27        37        47|       66        76    |   86        96       106       116       126       136       146  |    156       166       176       186       196       206       216       226       236       246       256       266    
                                                        47|                      81-L5P                                                             149-LRK                                                                                                                     
                                                         57                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhhhhhhhhhhh..eeee.........hhhhhhhhhhhh...eee.....hhhhhhhhhhhh..eeee.............hhhhh...eeeee.hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhh....eee......hhhhhhhhhhh....eee.hhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wxz B  19 GGVIMDVVNAEQAKIAEAAGAVAVMALERGVARMADPTVIEEVMNAVSIPVMAkVRIGHYVEARVLEALGVDYIDESEVLTPADEEFHIDKRQFTVPFVCGCRDLGEAARRIAEGASMLRTkGEPGTGNIVEAVRHMRKVNAQIRKVVNMSEDELVAEAKQLGAPVEVLREIKRLGRLPVVNFAAGGVTTPADAALMMHLGADGVFVGSGIFKSENPEKYARAIVEATTHYEDYELIAHLSKG 270
                                    28        38        57        67        77   |    87        97       107       117       127       137       147 |     157       167       177       187       197       207       217       227       237       247       257       267   
                                                       47|                      81-L5P                                                             149-LRK                                                                                                                     
                                                        57                                                                                                                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh....eeeee.hhhhhhhhhhhh..eeee.........hhhhhhhhhhhh...eee.....hhhhhhhhhhh...eeee.............hhhhh...eeeee.hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh....eee......hhhhhhhhhhh....eee.hhhhhh.hhhhhhhhhhhhhhh..hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wxz C   6 TDRVKRGMAEMQKGGVIMDVVNAEQAKIAEAAGAVAVMALEGGVARMADPTVIEEVMNAVSIPVMAkVRIGHYVEARVLEALGVDYIDESEVLTPADEEFHIDKRQFTVPFVCGCRDLGEAARRIAEGASMLRTkGEPGTGNIVEAVRHMRKVNAQIRKVVNMSEDELVAEAKQLGAPVEVLREIKRLGRLPVVNFAAGGVTTPADAALMMHLGADGVFVGSGIFKSENPEKYARAIVEATTHYEDYELIAHLSKG 270
                                    15        25        35        45||      64        74      | 84        94       104       114       124       134       144    |  154       164       174       184       194       204       214       224       234       244       254       264      
                                                                   46|                       81-L5P                                                             149-LRK                                                                                                                     
                                                                    56                                                                                                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:245
                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.hhhhhhhhhhhh..eeee........hhhhhhhhhhhh...eee.....hhhhhhhhhhh...eeee.............hhhhh...eeeee.hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhh....eee......hhhhhhhhhhh....eee.hhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wxz D  16 MQKGGVIMDVVNAEQAKIAEAAGAVAVMALEGVARMADPTVIEEVMNAVSIPVMAkVRIGHYVEARVLEALGVDYIDESEVLTPADEEFHIDKRQFTVPFVCGCRDLGEAARRIAEGASMLRTkGEPGTGNIVEAVRHMRKVNAQIRKVVNMSEDELVAEAKQLGAPVEVLREIKRLGRLPVVNFAAGGVTTPADAALMMHLGADGVFVGSGIFKSENPEKYARAIVEATTHYEDYELIAHLSKG 270
                                    25        35        45||      65        75     |  85        95       105       115       125       135       145   |   155       165       175       185       195       205       215       225       235       245       255       265     
                                                         46|                      81-L5P                                                             149-LRK                                                                                                                     
                                                          57                                                                                                                                                                                                                     


Chain E from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhhhhhhhhhhh..eeee........hhhhhhhhhhhh...eee.....hhhhhhhhhhhh..eeee.............hhhhh...eeeee.hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhh....eee......hhhhhhhhhhh....eee.hhhhhh.hhhhhhhhhhhhhhh..hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wxz E  18 KGGVIMDVVNAEQAKIAEAAGAVAVMALEGVARMADPTVIEEVMNAVSIPVMAkVRIGHYVEARVLEALGVDYIDESEVLTPADEEFHIDKRQFTVPFVCGCRDLGEAARRIAEGASMLRTkGEPGTGNIVEAVRHMRKVNAQIRKVVNMSEDELVAEAKQLGAPVEVLREIKRLGRLPVVNFAAGGVTTPADAALMMHLGADGVFVGSGIFKSENPEKYARAIVEATTHYEDYELIAHLSK 269
                                    27        37        57        67        77   |    87        97       107       117       127       137       147 |     157       167       177       187       197       207       217       227       237       247       257       267  
                                                       46|                      81-L5P                                                             149-LRK                                                                                                                    
                                                        57                                                                                                                                                                                                                    


Chain F from PDB  Type:PROTEIN  Length:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhhhhhhhhhhh..eeee.........hhhhhhhhhhhh...eee.....hhhhhhhhhhhh..eeee.............hhhhh...eeeee.hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh....eee......hhhhhhhhhhh....eee.hhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wxz F  18 KGGVIMDVVNAEQAKIAEAAGAVAVMALEGGVARMADPTVIEEVMNAVSIPVMAkVRIGHYVEARVLEALGVDYIDESEVLTPADEEFHIDKRQFTVPFVCGCRDLGEAARRIAEGASMLRTkGEPGTGNIVEAVRHMRKVNAQIRKVVNMSEDELVAEAKQLGAPVEVLREIKRLGRLPVVNFAAGGVTTPADAALMMHLGADGVFVGSGIFKSENPEKYARAIVEATTHYEDYELIAHLSKG 270
                                    27        37        56        66        76    |   86        96       106       116       126       136       146  |    156       166       176       186       196       206       216       226       236       246       256       266    
                                                       46|                       81-L5P                                                             149-LRK                                                                                                                     
                                                        56
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4WXZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WXZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WXZ)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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  4wxz
    Family and Domain Information: ProDom | SYSTERS
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  PDXS_GEOKA | Q5L3Y2
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  4.-.-.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
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 Related Entries

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

UniProtKB/Swiss-Prot
        PDXS_GEOKA | Q5L3Y2: 1znn 4wxy 4wy0

(-) Related Entries Specified in the PDB File

4wxz 4wy0