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 :  CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM THE PATHOGEN NEISSERIA MENINGITIDIS
 
Authors :  S. R. A. Devenish, A. T. Hadfield
Date :  19 Dec 08  (Deposition) - 23 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tim Barrel, Beta-Alpha-Barrel, Amino-Acid Biosynthesis, Diaminopimelate Biosynthesis, Lyase, Lysine Biosynthesis, Schiff Base (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. R. A. Devenish, F. H. A. Huisman, E. J. Parker, A. T. Hadfield, J. A. Gerrard
Cloning And Characterisation Of Dihydrodipicolinate Synthas From The Pathogen Neisseria Meningitidis.
Biochim. Biophys. Acta 2009
PubMed-ID: 19236959  |  Reference-DOI: 10.1016/J.BBAPAP.2009.02.003

(-) Compounds

Molecule 1 - DIHYDRODIPICOLINATE SYNTHASE
    Chains: A, B, C, D
    EC Number: 4.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-151/D
    Expression System Strain: BL21 STAR(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DAPA, NMB0929
    Organism Scientific: NEISSERIA MENINGITIDIS SEROGROUP B
    Organism Taxid: 491
    Strain: SEROGROUP B
    Synonym: DHDPS

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 47)

Asymmetric/Biological Unit (2, 47)
No.NameCountTypeFull Name
1GOL29Ligand/IonGLYCEROL
2SO418Ligand/IonSULFATE ION

(-) Sites  (47, 47)

Asymmetric Unit (47, 47)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:80 , TYR A:106 , GOL A:298 , HOH A:309 , HOH A:452 , HOH A:891 , ASN B:80 , TYR B:106 , GOL B:297BINDING SITE FOR RESIDUE SO4 A 292
02AC2SOFTWARETYR A:133 , ARG A:138 , GLY A:186 , PHE A:244 , SO4 A:294 , HOH A:384BINDING SITE FOR RESIDUE SO4 A 293
03AC3SOFTWAREALA A:8 , GLY A:43 , THR A:44 , THR A:45 , LEU A:101 , TYR A:133 , LYS A:161 , ILE A:203 , SO4 A:293BINDING SITE FOR RESIDUE SO4 A 294
04AC4SOFTWARELEU A:213 , ARG A:235 , GLN A:290 , HOH A:378BINDING SITE FOR RESIDUE SO4 A 295
05AC5SOFTWAREHIS A:189 , HOH A:415 , HOH A:873BINDING SITE FOR RESIDUE SO4 A 296
06AC6SOFTWAREILE A:19 , HIS A:20 , TYR A:21 , GLU A:22 , ARG A:25 , HOH A:317BINDING SITE FOR RESIDUE GOL A 297
07AC7SOFTWARESER A:48 , ALA A:49 , TYR A:106 , SO4 A:292 , HOH A:361 , HOH A:362 , HOH A:363 , HOH A:509 , ASN B:80 , TYR B:107BINDING SITE FOR RESIDUE GOL A 298
08AC8SOFTWARETRP A:30 , ASN A:34 , PRO A:211 , LYS A:212 , HOH A:787 , HOH A:796BINDING SITE FOR RESIDUE GOL A 299
09AC9SOFTWARESER A:257BINDING SITE FOR RESIDUE GOL A 300
10BC1SOFTWAREASN A:14 , GLN A:15 , GLU A:263 , HIS A:265 , ASP C:29 , HIS C:66BINDING SITE FOR RESIDUE GOL A 301
11BC2SOFTWARESER A:111 , GLN A:112 , HOH A:364 , HOH A:368 , HOH A:624BINDING SITE FOR RESIDUE GOL A 302
12BC3SOFTWARETHR A:144 , ASN A:145 , ASP A:146 , SER A:169 , HOH A:772BINDING SITE FOR RESIDUE GOL A 303
13BC4SOFTWAREMET B:1 , GLU B:179 , GLY B:180 , HIS B:200 , HOH B:398BINDING SITE FOR RESIDUE SO4 B 292
14BC5SOFTWAREALA B:8 , GLY B:43 , THR B:44 , THR B:45 , LEU B:101 , TYR B:133 , LYS B:161 , ILE B:203 , SO4 B:295BINDING SITE FOR RESIDUE SO4 B 293
15BC6SOFTWAREHIS B:189 , HOH B:363BINDING SITE FOR RESIDUE SO4 B 294
16BC7SOFTWARETYR B:133 , ARG B:138 , GLY B:186 , PHE B:244 , SO4 B:293BINDING SITE FOR RESIDUE SO4 B 295
17BC8SOFTWAREGLU A:275 , HOH A:645 , TRP B:254 , SER B:257 , ALA B:258 , PRO B:264BINDING SITE FOR RESIDUE GOL B 296
18BC9SOFTWAREASN A:80 , TYR A:107 , SO4 A:292 , SER B:48 , ALA B:49 , TYR B:106 , HOH B:302 , HOH B:304 , HOH B:351 , HOH B:705BINDING SITE FOR RESIDUE GOL B 297
19CC1SOFTWAREARG B:230 , GLU B:231 , ASP B:234 , HOH B:447 , ASN D:175BINDING SITE FOR RESIDUE GOL B 298
20CC2SOFTWARELYS A:286 , HOH A:329 , TRP B:30 , ARG B:261 , HOH B:395 , HOH B:518 , HOH B:570BINDING SITE FOR RESIDUE GOL B 299
21CC3SOFTWARESER B:111 , GLN B:112 , HOH B:357 , HOH B:358 , HOH B:614 , HOH B:644BINDING SITE FOR RESIDUE GOL B 300
22CC4SOFTWARETHR B:144 , ASN B:145 , ASP B:146 , SER B:169BINDING SITE FOR RESIDUE GOL B 301
23CC5SOFTWARETHR C:144 , ASN C:145 , SER C:169 , HOH C:330 , HOH C:352BINDING SITE FOR RESIDUE SO4 C 292
24CC6SOFTWAREASN C:80 , TYR C:106 , GOL C:298 , HOH C:315 , ASN D:80 , TYR D:106 , GOL D:295 , HOH D:369BINDING SITE FOR RESIDUE SO4 C 293
25CC7SOFTWAREALA C:8 , GLY C:43 , THR C:44 , THR C:45 , LEU C:101 , TYR C:133 , LYS C:161 , ILE C:203 , SO4 C:297 , GOL C:303BINDING SITE FOR RESIDUE SO4 C 294
26CC8SOFTWAREGLY C:180 , HIS C:200 , HOH C:367BINDING SITE FOR RESIDUE SO4 C 295
27CC9SOFTWAREHIS C:189 , PHE C:244 , HOH C:397 , HOH C:723BINDING SITE FOR RESIDUE SO4 C 296
28DC1SOFTWARETYR C:133 , ARG C:138 , LYS C:161 , PHE C:244 , SO4 C:294 , HOH C:321BINDING SITE FOR RESIDUE SO4 C 297
29DC2SOFTWARESER C:48 , ALA C:49 , GLY C:78 , TYR C:106 , SO4 C:293 , GOL C:303 , HOH C:946 , ASN D:80 , TYR D:107BINDING SITE FOR RESIDUE GOL C 298
30DC3SOFTWARETRP C:254 , SER C:257BINDING SITE FOR RESIDUE GOL C 299
31DC4SOFTWAREGLU B:22 , ARG B:25 , HOH B:487 , ASN C:145 , ASP C:146 , LEU C:149 , GLU C:172BINDING SITE FOR RESIDUE GOL C 300
32DC5SOFTWARETHR C:274 , GLU C:275 , ASN C:276BINDING SITE FOR RESIDUE GOL C 301
33DC6SOFTWARETRP C:30 , ASN C:34 , PRO C:211 , LYS C:212 , HOH C:362BINDING SITE FOR RESIDUE GOL C 302
34DC7SOFTWAREVAL C:42 , GLY C:43 , THR C:44 , SER C:48 , GLY C:76 , THR C:77 , GLY C:78 , LEU C:101 , SER C:102 , VAL C:103 , SO4 C:294 , GOL C:298 , HOH C:358 , TYR D:107BINDING SITE FOR RESIDUE GOL C 303
35DC8SOFTWARELYS C:109 , SO4 D:292 , SO4 D:294 , HOH D:379BINDING SITE FOR RESIDUE GOL C 304
36DC9SOFTWARESER C:111 , GLN C:112 , HOH C:369 , HOH C:603 , HOH C:765BINDING SITE FOR RESIDUE GOL C 305
37EC1SOFTWAREGOL C:304 , TYR D:133 , VAL D:135 , ARG D:138 , ALA D:163 , GLY D:186 , PHE D:244 , SO4 D:293BINDING SITE FOR RESIDUE SO4 D 292
38EC2SOFTWAREALA D:8 , GLY D:43 , THR D:44 , THR D:45 , LEU D:101 , TYR D:133 , LYS D:161 , ILE D:203 , SO4 D:292 , GOL D:296BINDING SITE FOR RESIDUE SO4 D 293
39EC3SOFTWAREGOL C:304 , HIS D:189 , HOH D:322 , HOH D:872BINDING SITE FOR RESIDUE SO4 D 294
40EC4SOFTWAREASN C:80 , SO4 C:293 , SER D:48 , ALA D:49 , GLY D:78 , TYR D:106 , GOL D:296 , HOH D:685 , HOH D:943BINDING SITE FOR RESIDUE GOL D 295
41EC5SOFTWARETYR C:107 , VAL D:42 , GLY D:43 , THR D:44 , SER D:48 , GLY D:76 , THR D:77 , GLY D:78 , LEU D:101 , SER D:102 , VAL D:103 , SO4 D:293 , GOL D:295 , HOH D:685BINDING SITE FOR RESIDUE GOL D 296
42EC6SOFTWAREHIS D:20 , TYR D:21 , GLU D:22 , ARG D:25 , HOH D:629BINDING SITE FOR RESIDUE GOL D 297
43EC7SOFTWAREHIS B:189 , ASP B:241 , HOH B:392 , ASN D:166 , GLY D:168 , SER D:169 , GLU D:172BINDING SITE FOR RESIDUE GOL D 298
44EC8SOFTWAREGLN A:90 , TRP D:254 , SER D:257 , PRO D:264 , HOH D:648BINDING SITE FOR RESIDUE GOL D 299
45EC9SOFTWAREASN D:14 , GLN D:15 , GLU D:263 , HIS D:265 , HOH D:802BINDING SITE FOR RESIDUE GOL D 300
46FC1SOFTWARETHR D:144 , ASN D:145 , ASP D:146 , SER D:169BINDING SITE FOR RESIDUE GOL D 301
47FC2SOFTWARESER D:111 , GLN D:112 , HOH D:331 , HOH D:364 , HOH D:686 , HOH D:747BINDING SITE FOR RESIDUE GOL D 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FLU)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ser A:248 -Pro A:249
2Leu A:268 -Pro A:269
3Ser B:248 -Pro B:249
4Leu B:268 -Pro B:269
5Ser C:248 -Pro C:249
6Leu C:268 -Pro C:269
7Ser D:248 -Pro D:249
8Leu D:268 -Pro D:269

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FLU)

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHDPS_1PS00665 Dihydrodipicolinate synthase signature 1.DAPA_NEIMB38-55
 
 
 		  4A:38-55
B:38-55
C:38-55
D:38-55
2DHDPS_2PS00666 Dihydrodipicolinate synthase signature 2.DAPA_NEIMB133-163
 
 
 		  4A:133-163
B:133-163
C:133-163
D:133-163

(-) Exons   (0, 0)

(no "Exon" information available for 3FLU)

(-) 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:294
 aligned with DAPA_NEIMB | Q9JZR4 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:294
                               1                                                                                                                                                                                                                                                                                                  
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287    
           DAPA_NEIMB     - ---MLQGSLVALITPMNQDGSIHYEQLRDLIDWHIENGTDGIVAVGTTGESATLSVEEHTAVIEAVVKHVAKRVPVIAGTGANNTVEAIALSQAAEKAGADYTLSVVPYYNKPSQEGIYQHFKTIAEATSIPMIIYNVPGRTVVSMTNDTILRLAEIPNIVGVKEASGNIGSNIELINRAPEGFVVLSGDDHTALPFMLCGGHGVITVAANAAPKLFADMCRAALQGDIALARELNDRLIPIYDTMFCEPSPAAPKWAVSALGRCEPHVRLPLVPLTENGQAKVRAALKASGQL 291
               SCOP domains d3flua_ A: automated matches                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3fluA00 A:-2-291 Aldolase class I                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee...........hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhh....eeeeee...hhhhhhhhhhhh....eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------DHDPS_1           -----------------------------------------------------------------------------DHDPS_2  PDB: A:133-163        -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3flu A  -2 PFTMLQGSLVALITPMNQDGSIHYEQLRDLIDWHIENGTDGIVAVGTTGESATLSVEEHTAVIEAVVKHVAKRVPVIAGTGANNTVEAIALSQAAEKAGADYTLSVVPYYNKPSQEGIYQHFKTIAEATSIPMIIYNVPGRTVVSMTNDTILRLAEIPNIVGVKEASGNIGSNIELINRAPEGFVVLSGDDHTALPFMLCGGHGVITVAANAAPKLFADMCRAALQGDIALARELNDRLIPIYDTMFCEPSPAAPKWAVSALGRCEPHVRLPLVPLTENGQAKVRAALKASGQL 291
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287    


Chain B from PDB  Type:PROTEIN  Length:291
 aligned with DAPA_NEIMB | Q9JZR4 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:291
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290 
           DAPA_NEIMB     1 MLQGSLVALITPMNQDGSIHYEQLRDLIDWHIENGTDGIVAVGTTGESATLSVEEHTAVIEAVVKHVAKRVPVIAGTGANNTVEAIALSQAAEKAGADYTLSVVPYYNKPSQEGIYQHFKTIAEATSIPMIIYNVPGRTVVSMTNDTILRLAEIPNIVGVKEASGNIGSNIELINRAPEGFVVLSGDDHTALPFMLCGGHGVITVAANAAPKLFADMCRAALQGDIALARELNDRLIPIYDTMFCEPSPAAPKWAVSALGRCEPHVRLPLVPLTENGQAKVRAALKASGQL 291
               SCOP domains d3flub_ B: automated matches                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3fluB00 B:1-291 Aldolase class I                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...........hhhhhhhhhhhhhhhh..eeee..........hhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhh....eeeeee...hhhhhhhhhhhh....eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------DHDPS_1           -----------------------------------------------------------------------------DHDPS_2  PDB: B:133-163        -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3flu B   1 MLQGSLVALITPMNQDGSIHYEQLRDLIDWHIENGTDGIVAVGTTGESATLSVEEHTAVIEAVVKHVAKRVPVIAGTGANNTVEAIALSQAAEKAGADYTLSVVPYYNKPSQEGIYQHFKTIAEATSIPMIIYNVPGRTVVSMTNDTILRLAEIPNIVGVKEASGNIGSNIELINRAPEGFVVLSGDDHTALPFMLCGGHGVITVAANAAPKLFADMCRAALQGDIALARELNDRLIPIYDTMFCEPSPAAPKWAVSALGRCEPHVRLPLVPLTENGQAKVRAALKASGQL 291
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290 


Chain C from PDB  Type:PROTEIN  Length:292
 aligned with DAPA_NEIMB | Q9JZR4 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:292
                             1                                                                                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289  
           DAPA_NEIMB     - -MLQGSLVALITPMNQDGSIHYEQLRDLIDWHIENGTDGIVAVGTTGESATLSVEEHTAVIEAVVKHVAKRVPVIAGTGANNTVEAIALSQAAEKAGADYTLSVVPYYNKPSQEGIYQHFKTIAEATSIPMIIYNVPGRTVVSMTNDTILRLAEIPNIVGVKEASGNIGSNIELINRAPEGFVVLSGDDHTALPFMLCGGHGVITVAANAAPKLFADMCRAALQGDIALARELNDRLIPIYDTMFCEPSPAAPKWAVSALGRCEPHVRLPLVPLTENGQAKVRAALKASGQL 291
               SCOP domains d3fluc_ C: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 3fluC00 C:0-291 Aldolase class I                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...........hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhh....eeeeee...hhhhhhhhhhhh....eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------DHDPS_1           -----------------------------------------------------------------------------DHDPS_2  PDB: C:133-163        -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3flu C   0 TMLQGSLVALITPMNQDGSIHYEQLRDLIDWHIENGTDGIVAVGTTGESATLSVEEHTAVIEAVVKHVAKRVPVIAGTGANNTVEAIALSQAAEKAGADYTLSVVPYYNKPSQEGIYQHFKTIAEATSIPMIIYNVPGRTVVSMTNDTILRLAEIPNIVGVKEASGNIGSNIELINRAPEGFVVLSGDDHTALPFMLCGGHGVITVAANAAPKLFADMCRAALQGDIALARELNDRLIPIYDTMFCEPSPAAPKWAVSALGRCEPHVRLPLVPLTENGQAKVRAALKASGQL 291
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289  


Chain D from PDB  Type:PROTEIN  Length:293
 aligned with DAPA_NEIMB | Q9JZR4 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:293
                              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   
           DAPA_NEIMB     - --MLQGSLVALITPMNQDGSIHYEQLRDLIDWHIENGTDGIVAVGTTGESATLSVEEHTAVIEAVVKHVAKRVPVIAGTGANNTVEAIALSQAAEKAGADYTLSVVPYYNKPSQEGIYQHFKTIAEATSIPMIIYNVPGRTVVSMTNDTILRLAEIPNIVGVKEASGNIGSNIELINRAPEGFVVLSGDDHTALPFMLCGGHGVITVAANAAPKLFADMCRAALQGDIALARELNDRLIPIYDTMFCEPSPAAPKWAVSALGRCEPHVRLPLVPLTENGQAKVRAALKASGQL 291
               SCOP domains d3flud_ D: automated matches                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3fluD00 D:-1-291 Aldolase class I                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...........hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhh....eeeeee...hhhhhhhhhhhh....eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------DHDPS_1           -----------------------------------------------------------------------------DHDPS_2  PDB: D:133-163        -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3flu D  -1 FTMLQGSLVALITPMNQDGSIHYEQLRDLIDWHIENGTDGIVAVGTTGESATLSVEEHTAVIEAVVKHVAKRVPVIAGTGANNTVEAIALSQAAEKAGADYTLSVVPYYNKPSQEGIYQHFKTIAEATSIPMIIYNVPGRTVVSMTNDTILRLAEIPNIVGVKEASGNIGSNIELINRAPEGFVVLSGDDHTALPFMLCGGHGVITVAANAAPKLFADMCRAALQGDIALARELNDRLIPIYDTMFCEPSPAAPKWAVSALGRCEPHVRLPLVPLTENGQAKVRAALKASGQL 291
                                     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
   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  (1, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FLU)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (DAPA_NEIMB | Q9JZR4)
molecular function
    GO:0008840    4-hydroxy-tetrahydrodipicolinate synthase    Catalysis of the reaction: pyruvate + L-aspartate-4-semialdehyde = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0019877    diaminopimelate biosynthetic process    The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.
    GO:0009085    lysine biosynthetic process    The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
    GO:0009089    lysine biosynthetic process via diaminopimelate    The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
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/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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
    CC5  [ RasMol ]  +environment [ RasMol ]
    CC6  [ RasMol ]  +environment [ RasMol ]
    CC7  [ RasMol ]  +environment [ RasMol ]
    CC8  [ RasMol ]  +environment [ RasMol ]
    CC9  [ RasMol ]  +environment [ RasMol ]
    DC1  [ RasMol ]  +environment [ RasMol ]
    DC2  [ RasMol ]  +environment [ RasMol ]
    DC3  [ RasMol ]  +environment [ RasMol ]
    DC4  [ RasMol ]  +environment [ RasMol ]
    DC5  [ RasMol ]  +environment [ RasMol ]
    DC6  [ RasMol ]  +environment [ RasMol ]
    DC7  [ RasMol ]  +environment [ RasMol ]
    DC8  [ RasMol ]  +environment [ RasMol ]
    DC9  [ RasMol ]  +environment [ RasMol ]
    EC1  [ RasMol ]  +environment [ RasMol ]
    EC2  [ RasMol ]  +environment [ RasMol ]
    EC3  [ RasMol ]  +environment [ RasMol ]
    EC4  [ RasMol ]  +environment [ RasMol ]
    EC5  [ RasMol ]  +environment [ RasMol ]
    EC6  [ RasMol ]  +environment [ RasMol ]
    EC7  [ RasMol ]  +environment [ RasMol ]
    EC8  [ RasMol ]  +environment [ RasMol ]
    EC9  [ RasMol ]  +environment [ RasMol ]
    FC1  [ RasMol ]  +environment [ RasMol ]
    FC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:268 - Pro A:269   [ RasMol ]  
    Leu B:268 - Pro B:269   [ RasMol ]  
    Leu C:268 - Pro C:269   [ RasMol ]  
    Leu D:268 - Pro D:269   [ RasMol ]  
    Ser A:248 - Pro A:249   [ RasMol ]  
    Ser B:248 - Pro B:249   [ RasMol ]  
    Ser C:248 - Pro C:249   [ RasMol ]  
    Ser D:248 - Pro D:249   [ RasMol ]  
 

(-) 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
  3flu
    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
  DAPA_NEIMB | Q9JZR4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.2.1.52
    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
  DAPA_NEIMB | Q9JZR4
    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 3FLU)

(-) Related Entries Specified in the PDB File

1yxc THE HOMOLOGOUS PROTEIN FROM E. COLI
1yxd THE HOMOLOGOUS PROTEIN FROM E. COLI SOAKED WITH THE INHIBITOR LYSINE