Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  L-GLUTAMATE DEHYDROGENASE FROM PYROBACULUM ISLANDICUM COMPLEXED WITH NAD
 
Authors :  M. W. Bhuiya, H. Sakuraba, T. Ohshima, T. Imagawa, N. Katunuma, H. Tsuge
Date :  26 Jan 04  (Deposition) - 14 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Protein-Nad Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. W. Bhuiya, H. Sakuraba, T. Ohshima, T. Imagawa, N. Katunuma, H. Tsuge
The First Crystal Structure Of Hyperthermostable Nad-Dependent Glutamate Dehydrogenase From Pyrobaculum Islandicum
J. Mol. Biol. V. 345 325 2005
PubMed-ID: 15571725  |  Reference-DOI: 10.1016/J.JMB.2004.10.063
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTAMATE DEHYDROGENASE
    Chains: A, B, C, D, E, F
    EC Number: 1.4.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROBACULUM ISLANDICUM
    Organism Taxid: 2277
    Synonym: HYPERTHERMOSTABLE NAD-DEPENDENT L-GLUTAMATE DEHYDROGENASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1NAD6Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:189 , GLN A:216 , GLY A:217 , GLY A:219 , ASN A:220 , VAL A:221 , ASP A:241 , ILE A:242 , ALA A:299 , ILE A:300 , GLY A:320 , ALA A:321 , ASN A:322 , ASN A:347 , HOH A:431BINDING SITE FOR RESIDUE NAD A 430
2AC2SOFTWARETHR B:189 , GLN B:216 , GLY B:219 , ASN B:220 , VAL B:221 , ASP B:241 , ILE B:242 , ALA B:299 , ALA B:321 , ASN B:322 , ASN B:347 , HOH B:1432BINDING SITE FOR RESIDUE NAD B 1430
3AC3SOFTWARETHR C:189 , GLY C:219 , ASN C:220 , VAL C:221 , SER C:240 , ASP C:241 , ILE C:242 , GLY C:265 , ALA C:299 , ILE C:300 , ALA C:321 , ASN C:322 , ASN C:347BINDING SITE FOR RESIDUE NAD C 2430
4AC4SOFTWARETHR D:189 , GLN D:216 , GLY D:219 , ASN D:220 , VAL D:221 , ASP D:241 , ILE D:242 , GLY D:265 , ALA D:298 , ALA D:299 , GLY D:320 , ALA D:321 , ASN D:322BINDING SITE FOR RESIDUE NAD D 3430
5AC5SOFTWARETHR E:189 , GLY E:217 , GLY E:219 , ASN E:220 , VAL E:221 , ASP E:241 , ILE E:242 , ALA E:299 , ILE E:300 , GLY E:320 , ALA E:321 , ASN E:322 , ASN E:347 , HOH E:4431BINDING SITE FOR RESIDUE NAD E 4430
6AC6SOFTWAREGLY F:219 , ASN F:220 , VAL F:221 , ASP F:241 , ILE F:242 , ALA F:298 , ALA F:299 , ILE F:300 , GLY F:320 , ALA F:321 , ASN F:322BINDING SITE FOR RESIDUE NAD F 5430

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V9L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V9L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V9L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V9L)

(-) Exons   (0, 0)

(no "Exon" information available for 1V9L)

(-) 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:418
 aligned with Q9Y8I4_PYRIS | Q9Y8I4 from UniProtKB/TrEMBL  Length:421

    Alignment length:418
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413        
         Q9Y8I4_PYRIS     4 TGFLEYVLNYVKKGVELGGFPEDFYKILSRPRRVLIVNIPVRLDGGGFEVFEGYRVQHCDVLGPYKGGVRFHPEVTLADDVALAILMTLKNSLAGLPYGGAKGAVRVDPKKLSQRELEELSRGYARAIAPLIGDVVDIPAPDVGTNAQIMAWMVDEYSKIKGYNVPGVFTSKPPELWGNPVREYATGFGVAVATREMAKKLWGGIEGKTVAIQGMGNVGRWTAYWLEKMGAKVIAVSDINGVAYRKEGLNVELIQKNKGLTGPALVELFTTKDNAEFVKNPDAIFKLDVDIFVPAAIENVIRGDNAGLVKARLVVEGANGPTTPEAERILYERGVVVVPDILANAGGVIMSYLEWVENLQWYIWDEEETRKRLENIMVNNVERVYKRWQREKGWTMRDAAIVTALERIYNAMKIRGWI 421
               SCOP domains d1v9la2 A:4-179 Glutamate dehydrogenase                                                                                                                                         d1v9la1 A:180-421 Glutamate dehydrogenase                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------1v9lA01 A:36-179 Leucine Dehydrogenase, chain A, domain 1                                                                                       1v9lA02 A:180-421 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh..hhhhhhhhhh..eeeeeeeeee.....eeeeeeeeeeee.....eeeeee.....hhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhh..hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhh...eeeeee....eee......hhhhhhh...hhhhhhhhhhhh.........hhhhhh...eeee..................eee.......hhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v9l A   4 TGFLEYVLNYVKKGVELGGFPEDFYKILSRPRRVLIVNIPVRLDGGGFEVFEGYRVQHCDVLGPYKGGVRFHPEVTLADDVALAILMTLKNSLAGLPYGGAKGAVRVDPKKLSQRELEELSRGYARAIAPLIGDVVDIPAPDVGTNAQIMAWMVDEYSKIKGYNVPGVFTSKPPELWGNPVREYATGFGVAVATREMAKKLWGGIEGKTVAIQGMGNVGRWTAYWLEKMGAKVIAVSDINGVAYRKEGLNVELIQKNKGLTGPALVELFTTKDNAEFVKNPDAIFKLDVDIFVPAAIENVIRGDNAGLVKARLVVEGANGPTTPEAERILYERGVVVVPDILANAGGVIMSYLEWVENLQWYIWDEEETRKRLENIMVNNVERVYKRWQREKGWTMRDAAIVTALERIYNAMKIRGWI 421
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413        


Chain B from PDB  Type:PROTEIN  Length:418
 aligned with Q9Y8I4_PYRIS | Q9Y8I4 from UniProtKB/TrEMBL  Length:421

    Alignment length:418
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413        
         Q9Y8I4_PYRIS     4 TGFLEYVLNYVKKGVELGGFPEDFYKILSRPRRVLIVNIPVRLDGGGFEVFEGYRVQHCDVLGPYKGGVRFHPEVTLADDVALAILMTLKNSLAGLPYGGAKGAVRVDPKKLSQRELEELSRGYARAIAPLIGDVVDIPAPDVGTNAQIMAWMVDEYSKIKGYNVPGVFTSKPPELWGNPVREYATGFGVAVATREMAKKLWGGIEGKTVAIQGMGNVGRWTAYWLEKMGAKVIAVSDINGVAYRKEGLNVELIQKNKGLTGPALVELFTTKDNAEFVKNPDAIFKLDVDIFVPAAIENVIRGDNAGLVKARLVVEGANGPTTPEAERILYERGVVVVPDILANAGGVIMSYLEWVENLQWYIWDEEETRKRLENIMVNNVERVYKRWQREKGWTMRDAAIVTALERIYNAMKIRGWI 421
               SCOP domains d1v9lb2 B:4-179 Glutamate dehydrogenase                                                                                                                                         d1v9lb1 B:180-421 Glutamate dehydrogenase                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------1v9lB01 B:36-179 Leucine Dehydrogenase, chain A, domain 1                                                                                       1v9lB02 B:180-421 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..eeeeeeeeee.....eeeeeeeeee.......eeeeeee....hhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh..hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhh...eeeee.............hhhhhhhhh...hhhhhhhhhhh..................eeee..................eee.......hhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v9l B   4 TGFLEYVLNYVKKGVELGGFPEDFYKILSRPRRVLIVNIPVRLDGGGFEVFEGYRVQHCDVLGPYKGGVRFHPEVTLADDVALAILMTLKNSLAGLPYGGAKGAVRVDPKKLSQRELEELSRGYARAIAPLIGDVVDIPAPDVGTNAQIMAWMVDEYSKIKGYNVPGVFTSKPPELWGNPVREYATGFGVAVATREMAKKLWGGIEGKTVAIQGMGNVGRWTAYWLEKMGAKVIAVSDINGVAYRKEGLNVELIQKNKGLTGPALVELFTTKDNAEFVKNPDAIFKLDVDIFVPAAIENVIRGDNAGLVKARLVVEGANGPTTPEAERILYERGVVVVPDILANAGGVIMSYLEWVENLQWYIWDEEETRKRLENIMVNNVERVYKRWQREKGWTMRDAAIVTALERIYNAMKIRGWI 421
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413        


Chain C from PDB  Type:PROTEIN  Length:418
 aligned with Q9Y8I4_PYRIS | Q9Y8I4 from UniProtKB/TrEMBL  Length:421

    Alignment length:418
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413        
         Q9Y8I4_PYRIS     4 TGFLEYVLNYVKKGVELGGFPEDFYKILSRPRRVLIVNIPVRLDGGGFEVFEGYRVQHCDVLGPYKGGVRFHPEVTLADDVALAILMTLKNSLAGLPYGGAKGAVRVDPKKLSQRELEELSRGYARAIAPLIGDVVDIPAPDVGTNAQIMAWMVDEYSKIKGYNVPGVFTSKPPELWGNPVREYATGFGVAVATREMAKKLWGGIEGKTVAIQGMGNVGRWTAYWLEKMGAKVIAVSDINGVAYRKEGLNVELIQKNKGLTGPALVELFTTKDNAEFVKNPDAIFKLDVDIFVPAAIENVIRGDNAGLVKARLVVEGANGPTTPEAERILYERGVVVVPDILANAGGVIMSYLEWVENLQWYIWDEEETRKRLENIMVNNVERVYKRWQREKGWTMRDAAIVTALERIYNAMKIRGWI 421
               SCOP domains d1v9lc2 C:4-179 Glutamate dehydrogenase                                                                                                                                         d1v9lc1 C:180-421 Glutamate dehydrogenase                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------1v9lC01 C:36-179 Leucine Dehydrogenase, chain A, domain 1                                                                                       1v9lC02 C:180-421 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh..hhhhhhhhhh..eeeeeeeeee.....eeeeeeeeee.......eeeeeee....hhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhh..hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh..eeeeeee..eeee......hhhhhhh...hhhhhhhhhhhh.......hhhhhhh....eeee..................eee.......hhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v9l C   4 TGFLEYVLNYVKKGVELGGFPEDFYKILSRPRRVLIVNIPVRLDGGGFEVFEGYRVQHCDVLGPYKGGVRFHPEVTLADDVALAILMTLKNSLAGLPYGGAKGAVRVDPKKLSQRELEELSRGYARAIAPLIGDVVDIPAPDVGTNAQIMAWMVDEYSKIKGYNVPGVFTSKPPELWGNPVREYATGFGVAVATREMAKKLWGGIEGKTVAIQGMGNVGRWTAYWLEKMGAKVIAVSDINGVAYRKEGLNVELIQKNKGLTGPALVELFTTKDNAEFVKNPDAIFKLDVDIFVPAAIENVIRGDNAGLVKARLVVEGANGPTTPEAERILYERGVVVVPDILANAGGVIMSYLEWVENLQWYIWDEEETRKRLENIMVNNVERVYKRWQREKGWTMRDAAIVTALERIYNAMKIRGWI 421
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413        


Chain D from PDB  Type:PROTEIN  Length:418
 aligned with Q9Y8I4_PYRIS | Q9Y8I4 from UniProtKB/TrEMBL  Length:421

    Alignment length:418
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413        
         Q9Y8I4_PYRIS     4 TGFLEYVLNYVKKGVELGGFPEDFYKILSRPRRVLIVNIPVRLDGGGFEVFEGYRVQHCDVLGPYKGGVRFHPEVTLADDVALAILMTLKNSLAGLPYGGAKGAVRVDPKKLSQRELEELSRGYARAIAPLIGDVVDIPAPDVGTNAQIMAWMVDEYSKIKGYNVPGVFTSKPPELWGNPVREYATGFGVAVATREMAKKLWGGIEGKTVAIQGMGNVGRWTAYWLEKMGAKVIAVSDINGVAYRKEGLNVELIQKNKGLTGPALVELFTTKDNAEFVKNPDAIFKLDVDIFVPAAIENVIRGDNAGLVKARLVVEGANGPTTPEAERILYERGVVVVPDILANAGGVIMSYLEWVENLQWYIWDEEETRKRLENIMVNNVERVYKRWQREKGWTMRDAAIVTALERIYNAMKIRGWI 421
               SCOP domains d1v9ld2 D:4-179 Glutamate dehydrogenase                                                                                                                                         d1v9ld1 D:180-421 Glutamate dehydrogenase                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------1v9lD01 D:36-179 Leucine Dehydrogenase, chain A, domain 1                                                                                       1v9lD02 D:180-421 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..eeeeeeeee.......eeeeeeeee.......ee..eee....hhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhhhhhhhhhhhhh....ee.......hhhhhhhhhhhhhhhhh..hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhh...eeeeee....eee......hhhhhhh...hhhhhhhhhhhh...eee...hhhhhh...eeee..................eee.......hhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v9l D   4 TGFLEYVLNYVKKGVELGGFPEDFYKILSRPRRVLIVNIPVRLDGGGFEVFEGYRVQHCDVLGPYKGGVRFHPEVTLADDVALAILMTLKNSLAGLPYGGAKGAVRVDPKKLSQRELEELSRGYARAIAPLIGDVVDIPAPDVGTNAQIMAWMVDEYSKIKGYNVPGVFTSKPPELWGNPVREYATGFGVAVATREMAKKLWGGIEGKTVAIQGMGNVGRWTAYWLEKMGAKVIAVSDINGVAYRKEGLNVELIQKNKGLTGPALVELFTTKDNAEFVKNPDAIFKLDVDIFVPAAIENVIRGDNAGLVKARLVVEGANGPTTPEAERILYERGVVVVPDILANAGGVIMSYLEWVENLQWYIWDEEETRKRLENIMVNNVERVYKRWQREKGWTMRDAAIVTALERIYNAMKIRGWI 421
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413        


Chain E from PDB  Type:PROTEIN  Length:418
 aligned with Q9Y8I4_PYRIS | Q9Y8I4 from UniProtKB/TrEMBL  Length:421

    Alignment length:418
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413        
         Q9Y8I4_PYRIS     4 TGFLEYVLNYVKKGVELGGFPEDFYKILSRPRRVLIVNIPVRLDGGGFEVFEGYRVQHCDVLGPYKGGVRFHPEVTLADDVALAILMTLKNSLAGLPYGGAKGAVRVDPKKLSQRELEELSRGYARAIAPLIGDVVDIPAPDVGTNAQIMAWMVDEYSKIKGYNVPGVFTSKPPELWGNPVREYATGFGVAVATREMAKKLWGGIEGKTVAIQGMGNVGRWTAYWLEKMGAKVIAVSDINGVAYRKEGLNVELIQKNKGLTGPALVELFTTKDNAEFVKNPDAIFKLDVDIFVPAAIENVIRGDNAGLVKARLVVEGANGPTTPEAERILYERGVVVVPDILANAGGVIMSYLEWVENLQWYIWDEEETRKRLENIMVNNVERVYKRWQREKGWTMRDAAIVTALERIYNAMKIRGWI 421
               SCOP domains d1v9le2 E:4-179 Glutamate dehydrogenase                                                                                                                                         d1v9le1 E:180-421 Glutamate dehydrogenase                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------1v9lE01 E:36-179 Leucine Dehydrogenase, chain A, domain 1                                                                                       1v9lE02 E:180-421 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh..hhhhhhhhh...eeeeeeeee.......eeeeeeeee.......eeeeeee....hhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhh..hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhh...eeeeeee..eeee......hhhhhh.....hhhhhhhhhhh...eee...hhhhh....eeee..........hhhhh...eee.......hhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v9l E   4 TGFLEYVLNYVKKGVELGGFPEDFYKILSRPRRVLIVNIPVRLDGGGFEVFEGYRVQHCDVLGPYKGGVRFHPEVTLADDVALAILMTLKNSLAGLPYGGAKGAVRVDPKKLSQRELEELSRGYARAIAPLIGDVVDIPAPDVGTNAQIMAWMVDEYSKIKGYNVPGVFTSKPPELWGNPVREYATGFGVAVATREMAKKLWGGIEGKTVAIQGMGNVGRWTAYWLEKMGAKVIAVSDINGVAYRKEGLNVELIQKNKGLTGPALVELFTTKDNAEFVKNPDAIFKLDVDIFVPAAIENVIRGDNAGLVKARLVVEGANGPTTPEAERILYERGVVVVPDILANAGGVIMSYLEWVENLQWYIWDEEETRKRLENIMVNNVERVYKRWQREKGWTMRDAAIVTALERIYNAMKIRGWI 421
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413        


Chain F from PDB  Type:PROTEIN  Length:418
 aligned with Q9Y8I4_PYRIS | Q9Y8I4 from UniProtKB/TrEMBL  Length:421

    Alignment length:418
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413        
         Q9Y8I4_PYRIS     4 TGFLEYVLNYVKKGVELGGFPEDFYKILSRPRRVLIVNIPVRLDGGGFEVFEGYRVQHCDVLGPYKGGVRFHPEVTLADDVALAILMTLKNSLAGLPYGGAKGAVRVDPKKLSQRELEELSRGYARAIAPLIGDVVDIPAPDVGTNAQIMAWMVDEYSKIKGYNVPGVFTSKPPELWGNPVREYATGFGVAVATREMAKKLWGGIEGKTVAIQGMGNVGRWTAYWLEKMGAKVIAVSDINGVAYRKEGLNVELIQKNKGLTGPALVELFTTKDNAEFVKNPDAIFKLDVDIFVPAAIENVIRGDNAGLVKARLVVEGANGPTTPEAERILYERGVVVVPDILANAGGVIMSYLEWVENLQWYIWDEEETRKRLENIMVNNVERVYKRWQREKGWTMRDAAIVTALERIYNAMKIRGWI 421
               SCOP domains d1v9lf2 F:4-179 Glutamate dehydrogenase                                                                                                                                         d1v9lf1 F:180-421 Glutamate dehydrogenase                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------1v9lF01 F:36-179 Leucine Dehydrogenase, chain A, domain 1                                                                                       1v9lF02 F:180-421 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                              CATH domains
           Pfam domains (1) ------------------------------ELFV_dehydrog_N-1v9lF07 F:34-164                                                                                                   ----------------ELFV_dehydrog-1v9lF01 F:181-419                                                                                                                                                                                                                -- Pfam domains (1)
           Pfam domains (2) ------------------------------ELFV_dehydrog_N-1v9lF08 F:34-164                                                                                                   ----------------ELFV_dehydrog-1v9lF02 F:181-419                                                                                                                                                                                                                -- Pfam domains (2)
           Pfam domains (3) ------------------------------ELFV_dehydrog_N-1v9lF09 F:34-164                                                                                                   ----------------ELFV_dehydrog-1v9lF03 F:181-419                                                                                                                                                                                                                -- Pfam domains (3)
           Pfam domains (4) ------------------------------ELFV_dehydrog_N-1v9lF10 F:34-164                                                                                                   ----------------ELFV_dehydrog-1v9lF04 F:181-419                                                                                                                                                                                                                -- Pfam domains (4)
           Pfam domains (5) ------------------------------ELFV_dehydrog_N-1v9lF11 F:34-164                                                                                                   ----------------ELFV_dehydrog-1v9lF05 F:181-419                                                                                                                                                                                                                -- Pfam domains (5)
           Pfam domains (6) ------------------------------ELFV_dehydrog_N-1v9lF12 F:34-164                                                                                                   ----------------ELFV_dehydrog-1v9lF06 F:181-419                                                                                                                                                                                                                -- Pfam domains (6)
         Sec.struct. author hhhhhhhhhhhhhhhhhh..hhhhhhhhh...eeeeeeeee.......eeeeeeeee.......eeeeeee....hhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhh..hhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhh..eeeeeee..eeee......hhhhhh.....hhhhhhhhhhh...eee............eeee..................eee.......hhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v9l F   4 TGFLEYVLNYVKKGVELGGFPEDFYKILSRPRRVLIVNIPVRLDGGGFEVFEGYRVQHCDVLGPYKGGVRFHPEVTLADDVALAILMTLKNSLAGLPYGGAKGAVRVDPKKLSQRELEELSRGYARAIAPLIGDVVDIPAPDVGTNAQIMAWMVDEYSKIKGYNVPGVFTSKPPELWGNPVREYATGFGVAVATREMAKKLWGGIEGKTVAIQGMGNVGRWTAYWLEKMGAKVIAVSDINGVAYRKEGLNVELIQKNKGLTGPALVELFTTKDNAEFVKNPDAIFKLDVDIFVPAAIENVIRGDNAGLVKARLVVEGANGPTTPEAERILYERGVVVVPDILANAGGVIMSYLEWVENLQWYIWDEEETRKRLENIMVNNVERVYKRWQREKGWTMRDAAIVTALERIYNAMKIRGWI 421
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413
   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  (2, 12)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 12)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 12)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: no clan defined [family: ELFV_dehydrog_N] (13)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Q9Y8I4_PYRIS | Q9Y8I4)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016639    oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    NAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1v9l)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1v9l
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q9Y8I4_PYRIS | Q9Y8I4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  1.4.1.2
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q9Y8I4_PYRIS | Q9Y8I4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1V9L)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1V9L)