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(-) Description

Title :  TAGATOSE-1,6-BISPHOSPHATE ALDOLASE FROM STREPTOCOCCUS PYOGENES IN COMPLEX WITH COMPETITIVE INHIBITOR HEXITOL-1,6-BISPHOSPHATE
 
Authors :  C. Lowkam
Date :  02 Dec 15  (Deposition) - 07 Dec 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Covalent Intermediate, Substrate, Aldolase, Lyase-Lyase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Lowkam, B. Liotard, J. Sygusch
Non-Stereospecific Substrate Cleavage By Tagatose-Bisphosphate Class I Aldolase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TAGATOSE 1,6-DIPHOSPHATE ALDOLASE 2
    Chains: A, B, C, D
    EC Number: 4.1.2.40
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LACD2, LACD.2, SPY_1919, M5005_SPY1635
    Organism Scientific: STREPTOCOCCUS PYOGENES SEROTYPE M1
    Organism Taxid: 301447
    Synonym: D-TAGATOSE-1,6-BISPHOSPHATE ALDOLASE 2,TAGATOSE-BISPHOSPHATE ALDOLASE 2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1CA10Ligand/IonCALCIUM ION
2M2P1Ligand/IonD-MANNITOL-1,6-DIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2M2P1Ligand/IonD-MANNITOL-1,6-DIPHOSPHATE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2M2P-1Ligand/IonD-MANNITOL-1,6-DIPHOSPHATE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:27 , GLN A:28 , ARG A:29 , GLY A:30 , ALA A:31 , THR A:94 , GLU A:163 , LYS A:205 , SER A:249 , ALA A:250 , LEU A:275 , CYS A:276 , GLY A:277 , ARG A:278 , HOH A:3117 , HOH A:3137 , HOH A:3140 , HOH A:3173 , HOH A:3203 , HOH A:3305binding site for residue M2P A 3001
02AC2SOFTWAREHOH A:3279 , HOH A:3323 , HOH A:3324 , HOH A:3418 , HOH B:735 , HOH B:921 , HOH B:929binding site for residue CA A 3002
03AC3SOFTWAREGLU A:238 , THR A:241 , HOH A:3123 , HOH A:3272 , GLU B:83 , GLU B:84binding site for residue CA A 3003
04AC4SOFTWAREHOH A:3350 , HOH D:783binding site for residue CA A 3004
05AC5SOFTWAREGLU A:83 , GLU A:84 , GLU B:238 , THR B:241 , HOH B:670binding site for residue CA B 401
06AC6SOFTWAREHOH A:3312 , HOH A:3449 , HOH A:3459 , HOH B:736 , HOH B:741 , HOH B:803 , HOH B:893binding site for residue CA B 402
07AC7SOFTWAREHOH B:742 , HOH B:875 , HOH B:877 , HOH B:992 , HOH C:729binding site for residue CA B 403
08AC8SOFTWAREALA B:37 , GLN B:40 , HOH B:589 , HOH B:780 , HOH B:881binding site for residue CA B 404
09AC9SOFTWAREGLU C:84 , HOH C:502 , HOH C:546 , HOH C:584 , HOH C:591binding site for residue CA C 401
10AD1SOFTWAREASP C:259 , HOH C:635 , HOH C:650 , ASP D:259 , HOH D:597 , HOH D:695binding site for residue CA D 401
11AD2SOFTWAREHOH D:683 , HOH D:715 , HOH D:735 , HOH D:785binding site for residue CA D 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F2M)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:3 -Leu A:4
2Pro C:44 -Thr C:45

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F2M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F2M)

(-) Exons   (0, 0)

(no "Exon" information available for 5F2M)

(-) 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:324
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.....eeeeee..hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhh......eeeee.....................hhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhh..........hhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5f2m A   3 TLTENKRKSMEKLSVDGVISALAFDQRGALKRMMAQHQTKEPTVEQIEELKSLVSEELTPFASSILLDPEYGLPASRVRSEEAGLLLAYEKTGYDATTTSRLPDCLDVWSAKRIKEAGAEAVKFLLYYDIDGDQDVNEQKKAYIERIGSECRAEDIPFYLEILTYDEKIADNASPEFAKVKAHKVNEAMKVFSKERFGVDVLKVEVPVNMKFVEGFADGEVLFTKEEAAQAFRDQEASTDLPYIYLSAGVSAKLFQDTLVFAAESGAKFNGVLCGRATWAGSVKVYIEEGPQAAREWLRTEGFKNIDELNKVLDKTASPWTEKM 326
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322    


Chain B from PDB  Type:PROTEIN  Length:324
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhh.....eeeeee..hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhh.....eeeee.....................hhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhh..........hhhhhhhhhhhhhh.....eee.....hhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5f2m B   2 ITLTENKRKSMEKLSVDGVISALAFDQRGALKRMMAQHQTKEPTVEQIEELKSLVSEELTPFASSILLDPEYGLPASRVRSEEAGLLLAYEKTGYDATTTSRLPDCLDVWSAKRIKEAGAEAVKFLLYYDIDGDQDVNEQKKAYIERIGSECRAEDIPFYLEILTYDEKIADNASPEFAKVKAHKVNEAMKVFSKERFGVDVLKVEVPVNMKFVEGFADGEVLFTKEEAAQAFRDQEASTDLPYIYLSAGVSAKLFQDTLVFAAESGAKFNGVLCGRATWAGSVKVYIEEGPQAAREWLRTEGFKNIDELNKVLDKTASPWTEK 325
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321    


Chain C from PDB  Type:PROTEIN  Length:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh.....eeeee....hhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.eeeehhhhhhhhhhh.....eeeee.....................hhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhh..........hhhhhhhhhhhhhh.....eee.....hhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f2m C   1 TITLTENKRKSMEKLSVDGVISALAFDQRGALKRMMAQHQTKEPTVEQIEELKSLVSEELTPFASSILLDPEYGLPASRVRSEEAGLLLAYEKTGYDATTTSRLPDCLDVWSAKRIKEAGAEAVKFLLYYDIDGDQDVNEQKKAYIERIGSECRAEDIPFYLEILTYDEKIADNASPEFAKVKAHKVNEAMKVFSKERFGVDVLKVEVPVNMKFVEGFADGEVLFTKEEAAQAFRDQEASTDLPYIYLSAGVSAKLFQDTLVFAAESGAKFNGVLCGRATWAGSVKVYIEEGPQAAREWLRTEGFKNIDELNKVLDKTASPWTEKM 326
                                    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       300       310       320      


Chain D from PDB  Type:PROTEIN  Length:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh.....eeeee....hhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhh.....eeeee.....................hhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhh..........hhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f2m D   1 TITLTENKRKSMEKLSVDGVISALAFDQRGALKRMMAQHQTKEPTVEQIEELKSLVSEELTPFASSILLDPEYGLPASRVRSEEAGLLLAYEKTGYDATTTSRLPDCLDVWSAKRIKEAGAEAVKFLLYYDIDGDQDVNEQKKAYIERIGSECRAEDIPFYLEILTYDEKIADNASPEFAKVKAHKVNEAMKVFSKERFGVDVLKVEVPVNMKFVEGFADGEVLFTKEEAAQAFRDQEASTDLPYIYLSAGVSAKLFQDTLVFAAESGAKFNGVLCGRATWAGSVKVYIEEGPQAAREWLRTEGFKNIDELNKVLDKTASPWTEKM 326
                                    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       300       310       320
   Legend:   → Mismatch (orange background)
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  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 5F2M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F2M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F2M)

(-) Gene Ontology  (8, 8)

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 Related Entries

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        LACD2_STRP1 | P63705: 3jrk 3mhf 3mhg 5f2g 5f2i 5f2l 5f4s 5f4w 5ff7

(-) Related Entries Specified in the PDB File

5f2g 5f2i 5f2j 5f2l 5f4s 5f4w 5f4x