Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF AQUIFEX AEOLICUS GIDA IN THE FORM II CRYSTAL
 
Authors :  T. Numata, T. Osawa
Date :  24 Dec 08  (Deposition) - 19 May 09  (Release) - 04 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Modification, Trna, 5-Carboxymethylaminomethyl Uridine, Wobble Uridine, Fad, Fad-Binding Protein, Trna Modification Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Osawa, K. Ito, H. Inanaga, O. Nureki, K. Tomita, T. Numata
Conserved Cysteine Residues Of Gida Are Essential For Biogenesis Of 5-Carboxymethylaminomethyluridine At Trna Anticodon
Structure V. 17 713 2009
PubMed-ID: 19446527  |  Reference-DOI: 10.1016/J.STR.2009.03.013

(-) Compounds

Molecule 1 - TRNA URIDINE 5-CARBOXYMETHYLAMINOMETHYL MODIFICATION ENZYME MNMG
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28B
    Expression System StrainBL21-CODONPLUS (DE3)-RIL
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneAQ_761
    Organism ScientificAQUIFEX AEOLICUS
    Organism Taxid63363
    SynonymGIDA, GLUCOSE-INHIBITED DIVISION PROTEIN A

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:13 , GLY A:14 , GLY A:15 , GLY A:16 , HIS A:17 , ALA A:18 , PHE A:36 , VAL A:37 , LEU A:38 , CYS A:48 , LYS A:57 , GLU A:124 , GLU A:125 , VAL A:126 , THR A:155 , THR A:156 , GLY A:157 , THR A:158 , PHE A:159 , SER A:181 , THR A:200 , GLY A:201 , TYR A:348 , ILE A:350 , GLY A:376 , ASN A:377 , THR A:382 , GLY A:383 , ALA A:387 , ARG A:434 , HOH A:619 , HOH A:623 , HOH A:626 , HOH A:635 , HOH A:655 , HOH A:659 , HOH A:665 , HOH A:672 , HOH A:713BINDING SITE FOR RESIDUE FAD A 618
2AC2SOFTWAREILE B:13 , GLY B:14 , GLY B:15 , GLY B:16 , HIS B:17 , ALA B:18 , VAL B:37 , LEU B:38 , CYS B:48 , LYS B:57 , GLU B:124 , GLU B:125 , VAL B:126 , THR B:155 , THR B:156 , GLY B:157 , THR B:158 , PHE B:159 , ARG B:175 , SER B:181 , THR B:200 , GLY B:201 , TYR B:348 , ILE B:350 , GLY B:376 , ASN B:377 , THR B:382 , GLY B:383 , TYR B:384 , ALA B:387 , ARG B:434 , HOH B:620 , HOH B:621 , HOH B:628 , HOH B:637 , HOH B:640 , HOH B:647 , HOH B:649 , HOH B:675 , HOH B:698 , HOH B:850 , HOH B:907BINDING SITE FOR RESIDUE FAD B 618
3AC3SOFTWAREILE C:13 , GLY C:14 , GLY C:15 , GLY C:16 , HIS C:17 , ALA C:18 , VAL C:37 , LEU C:38 , CYS C:48 , LYS C:57 , GLU C:124 , GLU C:125 , VAL C:126 , THR C:155 , THR C:156 , GLY C:157 , THR C:158 , PHE C:159 , ARG C:175 , SER C:181 , THR C:200 , GLY C:201 , TYR C:348 , ILE C:350 , GLY C:376 , ASN C:377 , THR C:382 , GLY C:383 , TYR C:384 , ALA C:387 , ARG C:434 , HOH C:619 , HOH C:620 , HOH C:622 , HOH C:626 , HOH C:628 , HOH C:644 , HOH C:649 , HOH C:653 , HOH C:654BINDING SITE FOR RESIDUE FAD C 618
4AC4SOFTWAREILE D:13 , GLY D:14 , GLY D:15 , GLY D:16 , HIS D:17 , ALA D:18 , PHE D:36 , VAL D:37 , LEU D:38 , CYS D:48 , LYS D:57 , GLU D:124 , GLU D:125 , VAL D:126 , THR D:155 , THR D:156 , GLY D:157 , THR D:158 , PHE D:159 , SER D:181 , THR D:200 , GLY D:201 , TYR D:348 , ILE D:350 , GLY D:376 , ASN D:377 , THR D:382 , GLY D:383 , ALA D:387 , ARG D:434 , HOH D:620 , HOH D:624 , HOH D:625 , HOH D:637 , HOH D:649 , HOH D:651 , HOH D:680 , HOH D:689 , HOH D:708 , HOH D:763BINDING SITE FOR RESIDUE FAD D 618

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZXI)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Asp A:223 -Pro A:224
2Glu A:233 -Pro A:234
3Asp B:223 -Pro B:224
4Glu B:233 -Pro B:234
5Asp C:223 -Pro C:224
6Glu C:233 -Pro C:234
7Asp D:223 -Pro D:224
8Glu D:233 -Pro D:234

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZXI)

(-) PROSITE Motifs  (2, 8)

Asymmetric Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GIDA_1PS01280 Glucose inhibited division protein A family signature 1.MNMG_AQUAE280-294
 
 
 
  4A:282-294
B:282-294
C:282-294
D:282-294
2GIDA_2PS01281 Glucose inhibited division protein A family signature 2.MNMG_AQUAE375-398
 
 
 
  4A:375-398
B:375-398
C:375-398
D:375-398
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GIDA_1PS01280 Glucose inhibited division protein A family signature 1.MNMG_AQUAE280-294
 
 
 
  2A:282-294
B:282-294
-
-
2GIDA_2PS01281 Glucose inhibited division protein A family signature 2.MNMG_AQUAE375-398
 
 
 
  2A:375-398
B:375-398
-
-
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GIDA_1PS01280 Glucose inhibited division protein A family signature 1.MNMG_AQUAE280-294
 
 
 
  2-
-
C:282-294
D:282-294
2GIDA_2PS01281 Glucose inhibited division protein A family signature 2.MNMG_AQUAE375-398
 
 
 
  2-
-
C:375-398
D:375-398

(-) Exons   (0, 0)

(no "Exon" information available for 2ZXI)

(-) 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:602
 aligned with MNMG_AQUAE | O66962 from UniProtKB/Swiss-Prot  Length:617

    Alignment length:617
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       
           MNMG_AQUAE     - --MAWVVDEFDVVVIGGGHAGIEAALAAARMGAKTAMFVLNADTIGQMSCNPAIGGIAKGIVVREIDALGGEMGKAIDQTGIQFKMLNTRKGKAVQSPRAQADKKRYREYMKKVCENQENLYIKQEEVVDIIVKNNQVVGVRTNLGVEYKTKAVVVTTGTFLNGVIYIGDKMIPGGRLGEPRSEGLSDFYRRFDFPLIRFKTGTPARLDKRTIDFSALEVAPGDDPPPKFSFWTEPVGSYWFPKGKEQVNCWITYTTPKTHEIIRKNLHRTALYGGLIKGIGPRYCPSIEDKIVKFPDKERHQIFLEPEGLDTIEIYPNGLSTSLPEEVQWEMYRSIPGLENVVLIRPAYAIEYDVVPPTELYPTLETKKIRGLFHAGNFNGTTGYEEAAGQGIVAGINAALRAFGKEPIYLRRDESYIGVMIDDLTTKGVTEPYRLFTSRSEYRLYIRQDNAILRLAKLGRELGLLSEEQYKLVKELEREIEKWKEFYKSERVSVAVGGDTRSYSVATLMTMNYTLDDVKEKFGYEVPQHPYVKEEVEIQLKYEPYIERERKLNEKLKKLEDTKIPPDIDYDKIPGLTKEAREKLKKFKPITVGQASRIDGITPAAITALLVYLGK 615
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh..eeee..hhhhhhhhhhhhhh...eeeee.hhhhh.......eee..hhhhhhhhhhhhh.hhhhhhhhheeeeeee....hhhhheeeeeehhhhhhhhhhhhhhh...eeeee..eeeeee....eeeeee....eee..eeee........eeee..eeee..........hhhhhhhhh....eeeeeee..eee.hhh.....eee.............................eeeee.hhhhhhhhhhh.---------------....hhhhhhhhh......eeeeee......eeeee......hhhhhhhhhh.........eee..eeeeeee.hhhhh...........eee.hhhhh..hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh.....hhhhh...........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeeehhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh...hhhhhhhhhhhh..hhhhhh.....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GIDA_1         --------------------------------------------------------------------------------GIDA_2  PDB: A:375-398  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zxi A  -1 SHMAWVVDEFDVVVIGGGHAGIEAALAAARMGAKTAMFVLNADTIGQMSCNPAIGGIAKGIVVREIDALGGEMGKAIDQTGIQFKMLNTRKGKAVQSPRAQADKKRYREYMKKVCENQENLYIKQEEVVDIIVKNNQVVGVRTNLGVEYKTKAVVVTTGTFLNGVIYIGDKMIPGGRLGEPRSEGLSDFYRRFDFPLIRFKTGTPARLDKRTIDFSALEVAPGDDPPPKFSFWTEPVGSYWFPKGKEQVNCWITYTTPKTHEIIRKNL---------------RYCPSIEDKIVKFPDKERHQIFLEPEGLDTIEIYPNGLSTSLPEEVQWEMYRSIPGLENVVLIRPAYAIEYDVVPPTELYPTLETKKIRGLFHAGNFNGTTGYEEAAGQGIVAGINAALRAFGKEPIYLRRDESYIGVMIDDLTTKGVTEPYRLFTSRSEYRLYIRQDNAILRLAKLGRELGLLSEEQYKLVKELEREIEKWKEFYKSERVSVAVGGDTRSYSVATLMTMNYTLDDVKEKFGYEVPQHPYVKEEVEIQLKYEPYIERERKLNEKLKKLEDTKIPPDIDYDKIPGLTKEAREKLKKFKPITVGQASRIDGITPAAITALLVYLGK 615
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       | -         -   |   288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       
                                                                                                                                                                                                                                                                                                     266             282                                                                                                                                                                                                                                                                                                                                             

Chain B from PDB  Type:PROTEIN  Length:606
 aligned with MNMG_AQUAE | O66962 from UniProtKB/Swiss-Prot  Length:617

    Alignment length:617
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       
           MNMG_AQUAE     - --MAWVVDEFDVVVIGGGHAGIEAALAAARMGAKTAMFVLNADTIGQMSCNPAIGGIAKGIVVREIDALGGEMGKAIDQTGIQFKMLNTRKGKAVQSPRAQADKKRYREYMKKVCENQENLYIKQEEVVDIIVKNNQVVGVRTNLGVEYKTKAVVVTTGTFLNGVIYIGDKMIPGGRLGEPRSEGLSDFYRRFDFPLIRFKTGTPARLDKRTIDFSALEVAPGDDPPPKFSFWTEPVGSYWFPKGKEQVNCWITYTTPKTHEIIRKNLHRTALYGGLIKGIGPRYCPSIEDKIVKFPDKERHQIFLEPEGLDTIEIYPNGLSTSLPEEVQWEMYRSIPGLENVVLIRPAYAIEYDVVPPTELYPTLETKKIRGLFHAGNFNGTTGYEEAAGQGIVAGINAALRAFGKEPIYLRRDESYIGVMIDDLTTKGVTEPYRLFTSRSEYRLYIRQDNAILRLAKLGRELGLLSEEQYKLVKELEREIEKWKEFYKSERVSVAVGGDTRSYSVATLMTMNYTLDDVKEKFGYEVPQHPYVKEEVEIQLKYEPYIERERKLNEKLKKLEDTKIPPDIDYDKIPGLTKEAREKLKKFKPITVGQASRIDGITPAAITALLVYLGK 615
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh..eeee..hhhhhhhhhhhhhh...eeeee.hhhhh.......eee..hhhhhhhhhhhhh.hhhhhhhhheeeeeee....hhhhheeeeeehhhhhhhhhhhhhhhh..eeeee..eeeeee....eeeeee....eee..eeee........eeee..eeee..........hhhhhhhhh....eeeeeee..eee.hhh.....eee.............................eeeee.hhhhhhhhhhh.....-----------...................eeeeee......eeeee......hhhhhhhhhh.........eee..eeeeeee.hhhhh...........eee.hhhhh..hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh.....hhhhh...........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..eeeee....eeeeehhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh...hhhhhhhhhhhh..hhhhhh.....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GIDA_1         --------------------------------------------------------------------------------GIDA_2  PDB: B:375-398  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zxi B  -1 SHMAWVVDEFDVVVIGGGHAGIEAALAAARMGAKTAMFVLNADTIGQMSCNPAIGGIAKGIVVREIDALGGEMGKAIDQTGIQFKMLNTRKGKAVQSPRAQADKKRYREYMKKVCENQENLYIKQEEVVDIIVKNNQVVGVRTNLGVEYKTKAVVVTTGTFLNGVIYIGDKMIPGGRLGEPRSEGLSDFYRRFDFPLIRFKTGTPARLDKRTIDFSALEVAPGDDPPPKFSFWTEPVGSYWFPKGKEQVNCWITYTTPKTHEIIRKNLHRTA-----------RYCPSIEDKIVKFPDKERHQIFLEPEGLDTIEIYPNGLSTSLPEEVQWEMYRSIPGLENVVLIRPAYAIEYDVVPPTELYPTLETKKIRGLFHAGNFNGTTGYEEAAGQGIVAGINAALRAFGKEPIYLRRDESYIGVMIDDLTTKGVTEPYRLFTSRSEYRLYIRQDNAILRLAKLGRELGLLSEEQYKLVKELEREIEKWKEFYKSERVSVAVGGDTRSYSVATLMTMNYTLDDVKEKFGYEVPQHPYVKEEVEIQLKYEPYIERERKLNEKLKKLEDTKIPPDIDYDKIPGLTKEAREKLKKFKPITVGQASRIDGITPAAITALLVYLGK 615
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268 |       -   |   288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       
                                                                                                                                                                                                                                                                                                         270         282                                                                                                                                                                                                                                                                                                                                             

Chain C from PDB  Type:PROTEIN  Length:604
 aligned with MNMG_AQUAE | O66962 from UniProtKB/Swiss-Prot  Length:617

    Alignment length:617
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       
           MNMG_AQUAE     - --MAWVVDEFDVVVIGGGHAGIEAALAAARMGAKTAMFVLNADTIGQMSCNPAIGGIAKGIVVREIDALGGEMGKAIDQTGIQFKMLNTRKGKAVQSPRAQADKKRYREYMKKVCENQENLYIKQEEVVDIIVKNNQVVGVRTNLGVEYKTKAVVVTTGTFLNGVIYIGDKMIPGGRLGEPRSEGLSDFYRRFDFPLIRFKTGTPARLDKRTIDFSALEVAPGDDPPPKFSFWTEPVGSYWFPKGKEQVNCWITYTTPKTHEIIRKNLHRTALYGGLIKGIGPRYCPSIEDKIVKFPDKERHQIFLEPEGLDTIEIYPNGLSTSLPEEVQWEMYRSIPGLENVVLIRPAYAIEYDVVPPTELYPTLETKKIRGLFHAGNFNGTTGYEEAAGQGIVAGINAALRAFGKEPIYLRRDESYIGVMIDDLTTKGVTEPYRLFTSRSEYRLYIRQDNAILRLAKLGRELGLLSEEQYKLVKELEREIEKWKEFYKSERVSVAVGGDTRSYSVATLMTMNYTLDDVKEKFGYEVPQHPYVKEEVEIQLKYEPYIERERKLNEKLKKLEDTKIPPDIDYDKIPGLTKEAREKLKKFKPITVGQASRIDGITPAAITALLVYLGK 615
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh..eeee..hhhhhhhhhhhhhh...eeeee.hhhhh.......eee..hhhhhhhhhhhhh.hhhhhhhhheeeeeee....hhhhheeeeeehhhhhhhhhhhhhhhh..eeeee..eeeeee....eeeeee....eee..eeee........eeee..eeee..........hhhhhhhhh....eeeeeee..eee.hhh.....eee.............................eeeee.hhhhhhhhhhh.....-----------...................eeeeee......eeeee......hhhhhhhhhh.........eee..eeeeeee.hhhhh...........eee.hhhhh..hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh.....hhhhh...........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..eeee...--.eeeehhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh...hhhhhhhhhhhh..hhhhhh.....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GIDA_1         --------------------------------------------------------------------------------GIDA_2  PDB: C:375-398  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zxi C  -1 SHMAWVVDEFDVVVIGGGHAGIEAALAAARMGAKTAMFVLNADTIGQMSCNPAIGGIAKGIVVREIDALGGEMGKAIDQTGIQFKMLNTRKGKAVQSPRAQADKKRYREYMKKVCENQENLYIKQEEVVDIIVKNNQVVGVRTNLGVEYKTKAVVVTTGTFLNGVIYIGDKMIPGGRLGEPRSEGLSDFYRRFDFPLIRFKTGTPARLDKRTIDFSALEVAPGDDPPPKFSFWTEPVGSYWFPKGKEQVNCWITYTTPKTHEIIRKNLHRTA-----------RYCPSIEDKIVKFPDKERHQIFLEPEGLDTIEIYPNGLSTSLPEEVQWEMYRSIPGLENVVLIRPAYAIEYDVVPPTELYPTLETKKIRGLFHAGNFNGTTGYEEAAGQGIVAGINAALRAFGKEPIYLRRDESYIGVMIDDLTTKGVTEPYRLFTSRSEYRLYIRQDNAILRLAKLGRELGLLSEEQYKLVKELEREIEKWKEFYKSERVSVAVG--TRSYSVATLMTMNYTLDDVKEKFGYEVPQHPYVKEEVEIQLKYEPYIERERKLNEKLKKLEDTKIPPDIDYDKIPGLTKEAREKLKKFKPITVGQASRIDGITPAAITALLVYLGK 615
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268 |       -   |   288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488        |- |     508       518       528       538       548       558       568       578       588       598       608       
                                                                                                                                                                                                                                                                                                         270         282                                                                                                                                                                                                                    497  |                                                                                                                   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               500                                                                                                                   

Chain D from PDB  Type:PROTEIN  Length:603
 aligned with MNMG_AQUAE | O66962 from UniProtKB/Swiss-Prot  Length:617

    Alignment length:617
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       
           MNMG_AQUAE     - --MAWVVDEFDVVVIGGGHAGIEAALAAARMGAKTAMFVLNADTIGQMSCNPAIGGIAKGIVVREIDALGGEMGKAIDQTGIQFKMLNTRKGKAVQSPRAQADKKRYREYMKKVCENQENLYIKQEEVVDIIVKNNQVVGVRTNLGVEYKTKAVVVTTGTFLNGVIYIGDKMIPGGRLGEPRSEGLSDFYRRFDFPLIRFKTGTPARLDKRTIDFSALEVAPGDDPPPKFSFWTEPVGSYWFPKGKEQVNCWITYTTPKTHEIIRKNLHRTALYGGLIKGIGPRYCPSIEDKIVKFPDKERHQIFLEPEGLDTIEIYPNGLSTSLPEEVQWEMYRSIPGLENVVLIRPAYAIEYDVVPPTELYPTLETKKIRGLFHAGNFNGTTGYEEAAGQGIVAGINAALRAFGKEPIYLRRDESYIGVMIDDLTTKGVTEPYRLFTSRSEYRLYIRQDNAILRLAKLGRELGLLSEEQYKLVKELEREIEKWKEFYKSERVSVAVGGDTRSYSVATLMTMNYTLDDVKEKFGYEVPQHPYVKEEVEIQLKYEPYIERERKLNEKLKKLEDTKIPPDIDYDKIPGLTKEAREKLKKFKPITVGQASRIDGITPAAITALLVYLGK 615
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------GIDA-2zxiD01 D:9-406                                                                                                                                                                                                                                                                                                                                                                                          -------------------------------------------------------------------------------------------------------------------------------------GIDA_assoc_3-2zxiD05 D:540-611                                          ---- Pfam domains (1)
           Pfam domains (2) ----------GIDA-2zxiD02 D:9-406                                                                                                                                                                                                                                                                                                                                                                                          -------------------------------------------------------------------------------------------------------------------------------------GIDA_assoc_3-2zxiD06 D:540-611                                          ---- Pfam domains (2)
           Pfam domains (3) ----------GIDA-2zxiD03 D:9-406                                                                                                                                                                                                                                                                                                                                                                                          -------------------------------------------------------------------------------------------------------------------------------------GIDA_assoc_3-2zxiD07 D:540-611                                          ---- Pfam domains (3)
           Pfam domains (4) ----------GIDA-2zxiD04 D:9-406                                                                                                                                                                                                                                                                                                                                                                                          -------------------------------------------------------------------------------------------------------------------------------------GIDA_assoc_3-2zxiD08 D:540-611                                          ---- Pfam domains (4)
         Sec.struct. author ....hhhhh..eeee..hhhhhhhhhhhhhh...eeeee.hhhhh.......eee..hhhhhhhhhhhhh.hhhhhhhhheeeeeee....hhhhheeeeeehhhhhhhhhhhhhhh...eeeee..eeeeee....eeeeee....eee..eeee........eeee..eeee..........hhhhhhhhh....eeeeeee..eee.hhh.....eee.............................eeeee.hhhhhhhhhhh..--------------....hhhhhhhhh......eeeeee......eeeee......hhhhhhhhhh.........eee..eeeeeee.hhhhh...........eee.hhhhh..hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh.....hhhhh...........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeeehhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh...hhhhhhhhhhhh..hhhhhh.....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GIDA_1         --------------------------------------------------------------------------------GIDA_2  PDB: D:375-398  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zxi D  -1 SHMAWVVDEFDVVVIGGGHAGIEAALAAARMGAKTAMFVLNADTIGQMSCNPAIGGIAKGIVVREIDALGGEMGKAIDQTGIQFKMLNTRKGKAVQSPRAQADKKRYREYMKKVCENQENLYIKQEEVVDIIVKNNQVVGVRTNLGVEYKTKAVVVTTGTFLNGVIYIGDKMIPGGRLGEPRSEGLSDFYRRFDFPLIRFKTGTPARLDKRTIDFSALEVAPGDDPPPKFSFWTEPVGSYWFPKGKEQVNCWITYTTPKTHEIIRKNLH--------------RYCPSIEDKIVKFPDKERHQIFLEPEGLDTIEIYPNGLSTSLPEEVQWEMYRSIPGLENVVLIRPAYAIEYDVVPPTELYPTLETKKIRGLFHAGNFNGTTGYEEAAGQGIVAGINAALRAFGKEPIYLRRDESYIGVMIDDLTTKGVTEPYRLFTSRSEYRLYIRQDNAILRLAKLGRELGLLSEEQYKLVKELEREIEKWKEFYKSERVSVAVGGDTRSYSVATLMTMNYTLDDVKEKFGYEVPQHPYVKEEVEIQLKYEPYIERERKLNEKLKKLEDTKIPPDIDYDKIPGLTKEAREKLKKFKPITVGQASRIDGITPAAITALLVYLGK 615
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258        |-         -   |   288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       
                                                                                                                                                                                                                                                                                                      267            282                                                                                                                                                                                                                                                                                                                                             

   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 2ZXI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZXI)

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Family: GIDA (2)
1aGIDA-2zxiD01D:9-406
1bGIDA-2zxiD02D:9-406
1cGIDA-2zxiD03D:9-406
1dGIDA-2zxiD04D:9-406

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (MNMG_AQUAE | O66962)
molecular function
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    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.
biological process
    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.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
    GO:0002098    tRNA wobble uridine modification    The process in which a uridine in position 34 of a tRNA is post-transcriptionally modified.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric 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
    FAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:223 - Pro A:224   [ RasMol ]  
    Asp B:223 - Pro B:224   [ RasMol ]  
    Asp C:223 - Pro C:224   [ RasMol ]  
    Asp D:223 - Pro D:224   [ RasMol ]  
    Glu A:233 - Pro A:234   [ RasMol ]  
    Glu B:233 - Pro B:234   [ RasMol ]  
    Glu C:233 - Pro C:234   [ RasMol ]  
    Glu D:233 - Pro D:234   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2zxi
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MNMG_AQUAE | O66962
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  MNMG_AQUAE | O66962
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MNMG_AQUAE | O669622zxh

(-) Related Entries Specified in the PDB File

2zxh