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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ALANINE:GLYOXYLATE AMINOTRANSFERASE MAJOR ALLELE (AGT-MA) AT 1.7 ANGSTROM; INTERNAL ALDIMINE WITH PLP IN THE ACTIVE SITE
 
Authors :  G. Giardina, F. Cutruzzola, C. Borri Voltattorni, B. Cellini, R. Mont
Date :  10 Dec 15  (Deposition) - 21 Dec 16  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminotransferase, Detoxification, Liver, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Giardina, F. Cutruzzola, C. Borri Voltattorni, B. Cellini, R. Montioli
X-Ray Induced Reduction Of Internal Aldimine At The Active Site Of Human Alanine:Glyoxylate Aminotransferase Major Allele
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SERINE--PYRUVATE AMINOTRANSFERASE
    Chains: A, B
    EC Number: 2.6.1.51, 2.6.1.44
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRCHIS2A
    Expression System Strain: JM109
    Expression System Taxid: 562
    Gene: AGXT, AGT1, SPAT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:81 , GLY A:82 , HIS A:83 , TRP A:108 , GLY A:156 , SER A:158 , ASP A:183 , VAL A:185 , ALA A:186 , GLN A:208 , LYS A:209 , TYR B:260 , THR B:263binding site for residue PLP A 401
2AC2SOFTWARETYR A:260 , THR A:263 , PRO B:28 , SER B:31 , SER B:81 , GLY B:82 , HIS B:83 , TRP B:108 , GLY B:156 , SER B:158 , ASP B:183 , VAL B:185 , ALA B:186 , SER B:207 , GLN B:208 , ALA B:210 , LEU B:211 , ASN B:212 , LEU B:364 , HOH B:634 , HOH B:648binding site for Di-peptide PLP B 401 and LYS B 209

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F9S)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:29 -Pro A:30
2Gly B:29 -Pro B:30

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F9S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F9S)

(-) Exons   (0, 0)

(no "Exon" information available for 5F9S)

(-) 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:385
                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.......ee........hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhh..eeeee.............hhhhhhhhh..eeeee..................eeeee...........eeeeehhhhhhhhhh..........hhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee...hhhhh...eeeee.....hhhhhhhhhhhhhhee....hhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f9s A   6 LLVTPPKALLKPLSIPNQLLLGPGPSNLPPRIMAAGGLQMIGSMSKDMYQIMDEIKEGIQYVFQTRNPLTLVISGSGHCALEAALVNVLEPGDSFLVGANGIWGQRAVDIGERIGARVHPMTKDPGGHYTLQEVEEGLAQHKPVLLFLTHGESSTGVLQPLDGFGELCHRYKCLLLVDSVASLGGTPLYMDRQGIDILYSGSQKALNAPPGTSLISFSDKAKKKMYSRKTKPFSFYLDIKWLANFWGCDDQPRMYHHTIPVISLYSLRESLALIAEQGLENSWRQHREAAAYLHGRLQALGLQLFVKDPALRLPTVTTVAVPAGYDWRDIVSYVIDHFDIEIMGGLGPSTGKVLRIGLLGCNATRENVDRVTEALRAALQHCPKK 390
                                    15        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       365       375       385     


Chain B from PDB  Type:PROTEIN  Length:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh.......ee........hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhh..eeeee.............hhhhhhhhh..eeeee..................eeeee...........eeeeehhhhhhhhhhh.........hhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh...eeeee.....hhhhhhhhhhhhhhee....hhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f9s B   6 LLVTPPKALLKPLSIPNQLLLGPGPSNLPPRIMAAGGLQMIGSMSKDMYQIMDEIKEGIQYVFQTRNPLTLVISGSGHCALEAALVNVLEPGDSFLVGANGIWGQRAVDIGERIGARVHPMTKDPGGHYTLQEVEEGLAQHKPVLLFLTHGESSTGVLQPLDGFGELCHRYKCLLLVDSVASLGGTPLYMDRQGIDILYSGSQKALNAPPGTSLISFSDKAKKKMYSRKTKPFSFYLDIKWLANFWGCDDQPRMYHHTIPVISLYSLRESLALIAEQGLENSWRQHREAAAYLHGRLQALGLQLFVKDPALRLPTVTTVAVPAGYDWRDIVSYVIDHFDIEIMGGLGPSTGKVLRIGLLGCNATRENVDRVTEALRAALQHCPKKK 391
                                    15        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       365       375       385
   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 5F9S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F9S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F9S)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        SPYA_HUMAN | P21549: 1h0c 1j04 2yob 3r9a 4cbr 4cbs 4i8a 4kxk 4kyo 5hhy

(-) Related Entries Specified in the PDB File

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