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(-) Description

Title :  STRUCTURE OF HUMAN PYCR-1 COMPLEXED WITH NADPH AND L-TETRAHYDROFUROIC ACID
 
Authors :  J. J. Tanner
Date :  20 Dec 16  (Deposition) - 15 Mar 17  (Release) - 10 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,C,D,E  (2x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Biol. Unit 4:  E  (2x)
Keywords :  Amino-Acid Biosynthesis, Oxidoreductase, Proline Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. M. Christensen, S. M. Patel, D. A. Korasick, A. C. Campbell, K. L. Krause, D. F. Becker, J. J. Tanner
Resolving The Cofactor-Binding Site In The Proline Biosynthetic Enzyme Human Pyrroline-5-Carboxylate Reductase 1.
J. Biol. Chem. V. 292 7233 2017
PubMed-ID: 28258219  |  Reference-DOI: 10.1074/JBC.M117.780288

(-) Compounds

Molecule 1 - PYRROLINE-5-CARBOXYLATE REDUCTASE 1, MITOCHONDRIAL
    ChainsA, B, C, D, E
    EC Number1.5.1.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 1-300
    GenePYCR1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymP5CR 1

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit ABCDE
Biological Unit 1 (2x)ABCDE
Biological Unit 2 (1x)AB   
Biological Unit 3 (1x)  CD 
Biological Unit 4 (2x)    E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1NDP5Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3TFB5Ligand/IonTETRAHYDROFURAN-2-CARBOXYLIC ACID
Biological Unit 1 (3, 22)
No.NameCountTypeFull Name
1NDP10Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
3TFB10Ligand/IonTETRAHYDROFURAN-2-CARBOXYLIC ACID
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
3TFB2Ligand/IonTETRAHYDROFURAN-2-CARBOXYLIC ACID
Biological Unit 3 (3, 5)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3TFB2Ligand/IonTETRAHYDROFURAN-2-CARBOXYLIC ACID
Biological Unit 4 (2, 4)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
3TFB2Ligand/IonTETRAHYDROFURAN-2-CARBOXYLIC ACID

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:7 , ALA A:8 , GLY A:9 , GLN A:10 , LEU A:11 , SER A:33 , SER A:34 , PRO A:35 , ASP A:36 , ASN A:56 , ALA A:69 , VAL A:70 , LYS A:71 , PRO A:72 , ILE A:78 , CYS A:95 , ALA A:96 , ALA A:97 , MET A:121 , THR A:122 , THR A:124 , HOH A:518 , HOH A:534 , HOH A:538 , HOH A:556 , HOH A:562 , ASN B:230 , VAL B:231 , TFB B:402 , HOH B:581binding site for residue NDP A 401
02AC2SOFTWAREGLY A:236 , ALA A:237 , THR A:238 , HOH A:501 , HOH A:508 , HOH A:539 , GLY B:175 , NDP B:401binding site for residue TFB A 402
03AC3SOFTWARETFB A:402 , HOH A:508 , HOH A:571 , GLY B:7 , ALA B:8 , GLY B:9 , GLN B:10 , LEU B:11 , SER B:33 , SER B:34 , PRO B:35 , ASP B:36 , ASN B:56 , ALA B:69 , VAL B:70 , LYS B:71 , PRO B:72 , ILE B:78 , CYS B:95 , ALA B:96 , ALA B:97 , MET B:121 , THR B:122 , THR B:124 , HOH B:512 , HOH B:513 , HOH B:514 , HOH B:554 , HOH B:557 , HOH B:564 , HOH B:575binding site for residue NDP B 401
04AC4SOFTWAREGLY A:175 , NDP A:401 , VAL B:231 , SER B:233 , ALA B:237 , THR B:238 , HOH B:503 , HOH B:533binding site for residue TFB B 402
05AC5SOFTWAREGLY C:7 , ALA C:8 , GLY C:9 , GLN C:10 , LEU C:11 , SER C:34 , PRO C:35 , ASP C:36 , MET C:37 , ASN C:56 , ALA C:69 , VAL C:70 , LYS C:71 , PRO C:72 , ILE C:78 , CYS C:95 , ALA C:96 , ALA C:97 , MET C:121 , THR C:122 , THR C:124 , HOH C:503 , HOH C:508 , HOH C:531 , HOH C:532 , HOH C:535 , HOH C:540 , HOH C:553 , HOH C:564 , HOH C:566 , HOH C:572 , HOH C:573 , HOH C:592 , HOH C:618 , VAL D:231 , TFB D:402binding site for residue NDP C 401
06AC6SOFTWARESER C:233 , ALA C:237 , THR C:238 , HOH C:515 , THR D:171 , GLY D:175 , NDP D:401 , HOH D:541binding site for residue TFB C 402
07AC7SOFTWAREASP B:64 , ARG B:89 , LEU C:39 , HOH C:600binding site for residue PEG C 403
08AC8SOFTWAREVAL C:231 , TFB C:402 , HOH C:565 , GLY D:7 , ALA D:8 , GLY D:9 , GLN D:10 , LEU D:11 , SER D:33 , SER D:34 , PRO D:35 , ASP D:36 , ASN D:56 , ALA D:69 , VAL D:70 , LYS D:71 , PRO D:72 , ILE D:78 , CYS D:95 , ALA D:96 , ALA D:97 , MET D:121 , THR D:122 , THR D:124 , HOH D:515 , HOH D:520 , HOH D:541 , HOH D:550 , HOH D:566 , HOH D:572 , HOH D:600binding site for residue NDP D 401
09AC9SOFTWARETHR C:171 , GLY C:175 , NDP C:401 , HOH C:508 , SER D:233 , GLY D:236 , ALA D:237 , THR D:238 , HOH D:502 , HOH D:526binding site for residue TFB D 402
10AD1SOFTWAREGLY E:7 , ALA E:8 , GLY E:9 , GLN E:10 , LEU E:11 , SER E:34 , PRO E:35 , ASP E:36 , MET E:37 , ASN E:56 , ALA E:69 , VAL E:70 , LYS E:71 , PRO E:72 , ILE E:78 , CYS E:95 , ALA E:96 , ALA E:97 , MET E:121 , THR E:122 , THR E:124 , ASN E:230 , VAL E:231 , TFB E:402 , HOH E:515 , HOH E:522 , HOH E:530 , HOH E:538 , HOH E:553 , HOH E:555 , HOH E:558 , HOH E:579 , HOH E:588binding site for residue NDP E 401
11AD2SOFTWARETHR E:171 , GLY E:175 , VAL E:231 , SER E:233 , ALA E:237 , THR E:238 , NDP E:401 , HOH E:515 , HOH E:550binding site for residue TFB E 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5UAV)

(-) 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:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee..hhhhhhhhhhhhhh...hhh.eeee.....hhhhhhhhhhh.eee.hhhhhhhhh.eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh.....eeeeee.hhhhhhh.eeeeeee....hhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uav A  -3 YFQSMSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMDLATVSALRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVSCAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVEDGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVKMGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHVLESGGFRSLLINAVEASCIRTRELQSMADQ 274
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266        

Chain B from PDB  Type:PROTEIN  Length:279
                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee..hhhhhhhhhhhhhh...hhh.eeee.....hhhhhhhhhhh.eee.hhhhhhhhh.eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh.....eeeeee.hhhhhhh.eeeeeee......hhhhhhhhhhhh.eeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uav B  -5 NLYFQSMSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMDLATVSALRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVSCAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVEDGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVKMGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHVLESGGFRSLLINAVEASCIRTRELQSMAD 273
                                     4        14        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         

Chain C from PDB  Type:PROTEIN  Length:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee..hhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhh.eee.hhhhhhhhh.eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh.....eeeeee.hhhhhhh.eeeeeee....hhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uav C  -3 YFQSMSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMDLATVSALRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVSCAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVEDGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVKMGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHVLESGGFRSLLINAVEASCIRTRELQSMAD 273
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       

Chain D from PDB  Type:PROTEIN  Length:279
                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee..hhhhhhhhhhhhhh...hhh.eeee.....hhhhhhhhhhh.eee.hhhhhhhhh.eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh.....eeeeee.hhhhhhh.eeeeeee......hhhhhhhhhhhh.eeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uav D  -5 NLYFQSMSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMDLATVSALRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVSCAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVEDGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVKMGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHVLESGGFRSLLINAVEASCIRTRELQSMAD 273
                                     4        14        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         

Chain E from PDB  Type:PROTEIN  Length:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhhhh..hhh.eeee....hhhhhhhhhhhh.eee.hhhhhhhhh.eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh.....eeeeee.hhhhhhh.eeeeeee....hhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uav E   0 SMSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMDLATVSALRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVSCAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVEDGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVKMGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHVLESGGFRSLLINAVEASCIRTRELQSMADQ 274
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269     

   Legend:   → Mismatch (orange background)
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    → 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 5UAV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        P5CR1_HUMAN | P323222ger 2gr9 2gra 2izz 5uat 5uau 5uaw 5uax

(-) Related Entries Specified in the PDB File

5uat 5uau 5uaw 5uax