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(-) Description

Title :  TAGATOSE-1,6-BISPHOSPHATE ALDOLASE FROM STREPTOCOCCUS PYOGENES IN COMPLEX WITH TBP
 
Authors :  C. Lowkam
Date :  03 Dec 15  (Deposition) - 01 Feb 17  (Release) - 01 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Covalent Intermediate, Acidic Ph, Substrate, Aldolase, Class I, Lyase (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): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
113P1Ligand/Ion1,3-DIHYDROXYACETONEPHOSPHATE
2CA4Ligand/IonCALCIUM ION
3CL4Ligand/IonCHLORIDE ION
4P6T1Ligand/Ion1,6-DI-O-PHOSPHONO-D-TAGATOSE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
113P1Ligand/Ion1,3-DIHYDROXYACETONEPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4P6T1Ligand/Ion1,6-DI-O-PHOSPHONO-D-TAGATOSE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
113P-1Ligand/Ion1,3-DIHYDROXYACETONEPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4P6T-1Ligand/Ion1,6-DI-O-PHOSPHONO-D-TAGATOSE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:27 , GLN A:28 , ARG A:29 , ALA A:31 , LEU A:68 , THR A:94 , LYS A:125 , GLU A:163 , LYS A:205 , LEU A:248 , SER A:249 , ALA A:250 , LEU A:275 , GLY A:277 , ARG A:278 , CL A:3002 , 13P A:3003 , HOH A:3101 , HOH A:3103 , HOH A:3110 , HOH A:3111 , HOH A:3119 , HOH A:3226 , HOH A:3332 , HOH A:3396binding site for residue P6T A 3001
02AC2SOFTWAREGLN A:28 , ARG A:29 , GLY A:30 , ALA A:31 , THR A:94 , P6T A:3001 , HOH A:3332binding site for residue CL A 3002
03AC3SOFTWAREASP A:27 , GLN A:28 , LEU A:68 , LYS A:125 , GLU A:163 , LYS A:205 , LEU A:248 , SER A:249 , ALA A:250 , LEU A:275 , GLY A:277 , ARG A:278 , P6T A:3001 , HOH A:3110binding site for residue 13P A 3003
04AC4SOFTWAREHOH A:3423 , HOH C:839 , HOH C:905 , HOH C:931binding site for residue CA A 3004
05AC5SOFTWAREGLU A:238 , THR A:241 , GLU C:83 , GLU C:84 , HOH C:777binding site for residue CA A 3005
06AC6SOFTWAREARG B:29 , GLY B:30 , ALA B:31binding site for residue CL B 401
07AC7SOFTWAREALA C:37 , GLN C:40 , HOH C:814binding site for residue CA C 401
08AC8SOFTWAREARG C:29 , GLY C:30 , ALA C:31binding site for residue CL C 402
09AC9SOFTWAREGLU D:84 , HOH D:528 , HOH D:532 , HOH D:679 , HOH D:734binding site for residue CA D 401
10AD1SOFTWAREARG D:29 , GLY D:30 , ALA D:31 , HOH D:631binding site for residue CL D 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F4W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5F4W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F4W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F4W)

(-) Exons   (0, 0)

(no "Exon" information available for 5F4W)

(-) 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:325
                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh....eeeeee..hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhh.....eeeee.....................hhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhh..........hhhhhhhhhhhhhh.....eee.....hhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f4w A   2 ITLTENKRKSMEKLSVDGVISALAFDQRGALKRMMAQHQTKEPTVEQIEELKSLVSEELTPFASSILLDPEYGLPASRVRSEEAGLLLAYEKTGYDATTTSRLPDCLDVWSAKRIKEAGAEAVKFLLYYDIDGDQDVNEQKKAYIERIGSECRAEDIPFYLEILTYDEKIADNASPEFAKVKAHKVNEAMKVFSKERFGVDVLKVEVPVNMKFVEGFADGEVLFTKEEAAQAFRDQEASTDLPYIYLSAGVSAKLFQDTLVFAAESGAKFNGVLCGRATWAGSVKVYIEEGPQAAREWLRTEGFKNIDELNKVLDKTASPWTEKM 326
                                    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 B from PDB  Type:PROTEIN  Length:325
                                                                                                                                                                                                                                                                                                                                                                     
               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....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f4w B   2 ITLTENKRKSMEKLSVDGVISALAFDQRGALKRMMAQHQTKEPTVEQIEELKSLVSEELTPFASSILLDPEYGLPASRVRSEEAGLLLAYEKTGYDATTTSRLPDCLDVWSAKRIKEAGAEAVKFLLYYDIDGDQDVNEQKKAYIERIGSECRAEDIPFYLEILTYDEKIADNASPEFAKVKAHKVNEAMKVFSKERFGVDVLKVEVPVNMKFVEGFADGEVLFTKEEAAQAFRDQEASTDLPYIYLSAGVSAKLFQDTLVFAAESGAKFNGVLCGRATWAGSVKVYIEEGPQAAREWLRTEGFKNIDELNKVLDKTASPWTEKM 326
                                    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.....eeeeee..hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhh.....eeeee.....................hhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhh..........hhhhhhhhhhhhhh.....eee.....hhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f4w 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.....eeeeee..hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhh.....eeeee.....................hhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhh..........hhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f4w 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 5F4W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F4W)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (8, 8)

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        LACD2_STRP1 | P63705: 3jrk 3mhf 3mhg 5f2g 5f2i 5f2l 5f2m 5f4s 5ff7

(-) Related Entries Specified in the PDB File

5f2g 5f2i 5f2j 5f2l 5f2m 5f4s 5f4x