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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TRYPTOPHAN SYNTHASE BETA-SER178PRO MUTANT COMPLEXED WITH N-[1H-INDOL-3-YL-ACETYL]GLYCINE ACID
 
Authors :  M. Weyand, I. Schlichting, A. Marabotti, A. Mozzarelli
Date :  26 Oct 01  (Deposition) - 19 Jun 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Carbon-Oxygen Lyase, Tryptophan Biosynthesis, Pyridoxal Phosphate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Weyand, I. Schlichting, P. Herde, A. Marabotti, A. Mozzarelli
Crystal Structure Of The Beta Ser178--> Pro Mutant Of Tryptophan Synthase. A "Knock-Out" Allosteric Enzyme.
J. Biol. Chem. V. 277 10653 2002
PubMed-ID: 11756454  |  Reference-DOI: 10.1074/JBC.M111031200

(-) Compounds

Molecule 1 - TRYPTOPHAN SYNTHASE ALPHA CHAIN
    ChainsA
    EC Number4.2.1.20
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPSTB7
    Expression System StrainCB149
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneTRPA/TRPB
    Organism ScientificSALMONELLA TYPHIMURIUM
    Organism Taxid602
 
Molecule 2 - TRYPTOPHAN SYNTHASE BETA CHAIN
    ChainsB
    EC Number4.2.1.20
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPSTB7
    Expression System StrainCB149
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneTRPA/TRPB
    MutationYES
    Organism ScientificSALMONELLA TYPHIMURIUM
    Organism Taxid602

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1IAG1Ligand/IonN-[1H-INDOL-3-YL-ACETYL]GLYCINE ACID
2NA1Ligand/IonSODIUM ION
3PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1IAG2Ligand/IonN-[1H-INDOL-3-YL-ACETYL]GLYCINE ACID
2NA-1Ligand/IonSODIUM ION
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:232 , PHE B:306 , SER B:308 , HOH B:511 , HOH B:623BINDING SITE FOR RESIDUE NA B 503
2AC2SOFTWAREPHE A:22 , GLU A:49 , ASP A:60 , ILE A:64 , LEU A:100 , TYR A:175 , PHE A:212 , GLY A:234 , SER A:235 , HOH A:545BINDING SITE FOR RESIDUE IAG A 501
3AC3SOFTWAREHIS B:86 , LYS B:87 , GLN B:114 , THR B:190 , CYS B:230 , GLY B:232 , GLY B:233 , GLY B:234 , SER B:235 , ASN B:236 , GLY B:303 , GLU B:350 , SER B:377 , GLY B:378 , HOH B:520 , HOH B:680BINDING SITE FOR RESIDUE PLP B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K8Z)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asp A:27 -Pro A:28
2Arg B:55 -Pro B:56
3His B:195 -Pro B:196

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K8Z)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRP_SYNTHASE_ALPHAPS00167 Tryptophan synthase alpha chain signature.TRPA_SALTY48-61  1A:48-61
2TRP_SYNTHASE_BETAPS00168 Tryptophan synthase beta chain pyridoxal-phosphate attachment site.TRPB_SALTY80-94  1B:80-94
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRP_SYNTHASE_ALPHAPS00167 Tryptophan synthase alpha chain signature.TRPA_SALTY48-61  2A:48-61
2TRP_SYNTHASE_BETAPS00168 Tryptophan synthase beta chain pyridoxal-phosphate attachment site.TRPB_SALTY80-94  2B:80-94

(-) Exons   (0, 0)

(no "Exon" information available for 1K8Z)

(-) 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:257
 aligned with TRPA_SALTY | P00929 from UniProtKB/Swiss-Prot  Length:268

    Alignment length:268
                                    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        
           TRPA_SALTY     1 MERYENLFAQLNDRREGAFVPFVTLGDPGIEQSLKIIDTLIDAGADALELGVPFSDPLADGPTIQNANLRAFAAGVTPAQCFEMLALIREKHPTIPIGLLMYANLVFNNGIDAFYARCEQVGVDSVLVADVPVEESAPFRQAALRHNIAPIFICPPNADDDLLRQVASYGRGYTYLLSRSGVTGAENRGALPLHHLIEKLKEYHAAPALQGFGISSPEQVSAAVRAGAAGAISGSAIVKIIEKNLASPKQMLAELRSFVSAMKAASRA 268
               SCOP domains d1k8za_ A: Trp synthase alpha-subunit                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1k8zA00 A:1-268 Aldolase class I                                                                                                                                                                                                                                             CATH domains
               Pfam domains -------Trp_syntA-1k8zA01 A:8-267                                                                                                                                                                                                                                           - Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhh....eeee.........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh..ee..ee....hhhhhhhhhhhh...eeee.-----------..hhhhhhhhhhhh....eeee....hhhhhhhhhhh...eeeehhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------TRP_SYNTHASE_A--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k8z A   1 MERYENLFAQLNDRREGAFVPFVTLGDPGIEQSLKIIDTLIDAGADALELGVPFSDPLADGPTIQNANLRAFAAGVTPAQCFEMLALIREKHPTIPIGLLMYANLVFNNGIDAFYARCEQVGVDSVLVADVPVEESAPFRQAALRHNIAPIFICPPNADDDLLRQVASYGRGYTYLLS-----------ALPLHHLIEKLKEYHAAPALQGFGISSPEQVSAAVRAGAAGAISGSAIVKIIEKNLASPKQMLAELRSFVSAMKAASRA 268
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       | -       190       200       210       220       230       240       250       260        
                                                                                                                                                                                                           178         190                                                                              

Chain B from PDB  Type:PROTEIN  Length:394
 aligned with TRPB_SALTY | P0A2K1 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:394
                                    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       331       341       351       361       371       381       391    
           TRPB_SALTY     2 TTLLNPYFGEFGGMYVPQILMPALNQLEEAFVSAQKDPEFQAQFADLLKNYAGRPTALTKCQNITAGTRTTLYLKREDLLHGGAHKTNQVLGQALLAKRMGKSEIIAETGAGQHGVASALASALLGLKCRIYMGAKDVERQSPNVFRMRLMGAEVIPVHSGSATLKDACNEALRDWSGSYETAHYMLGTAAGPHPYPTIVREFQRMIGEETKAQILDKEGRLPDAVIACVGGGSNAIGMFADFINDTSVGLIGVEPGGHGIETGEHGAPLKHGRVGIYFGMKAPMMQTADGQIEESYSISAGLDFPSVGPQHAYLNSIGRADYVSITDDEALEAFKTLCRHEGIIPALESSHALAHALKMMREQPEKEQLLVVNLSGRGDKDIFTVHDILKARG 395
               SCOP domains d1k8zb_ B: Tryptophan synthase, beta-subunit                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------1k8zB01 B:9-53,B:87-205                      1k8zB02 B:54-86,B:206-391        1k8zB01 B:9-53,B:87-205  [code=3.40.50.1100, no name defined]                                                          1k8zB02 B:54-86,B:206-391  [code=3.40.50.1100, no name defined]                                                                                                                           ---- CATH domains
               Pfam domains ------------------------------------------------PALP-1k8zB01 B:50-378                                                                                                                                                                                                                                                                                                                    ----------------- Pfam domains
         Sec.struct. author ......ee..eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eee.........eeeeeee.hhh.....hhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh...eeee........hhhhhhhhh.hhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.....eeeeeeeee.hhhhh...hhhhhheeeee.eeeeee..............hhhhh....hhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------TRP_SYNTHASE_BE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k8z B   2 TTLLNPYFGEFGGMYVPQILMPALNQLEEAFVSAQKDPEFQAQFADLLKNYAGRPTALTKCQNITAGTRTTLYLKREDLLHGGAHKTNQVLGQALLAKRMGKSEIIAETGAGQHGVASALASALLGLKCRIYMGAKDVERQSPNVFRMRLMGAEVIPVHSGSATLKDACNEALRDWPGSYETAHYMLGTAAGPHPYPTIVREFQRMIGEETKAQILDKEGRLPDAVIACVGGGSNAIGMFADFINDTSVGLIGVEPGGHGIETGEHGAPLKHGRVGIYFGMKAPMMQTADGQIEESYSISAGLDFPSVGPQHAYLNSIGRADYVSITDDEALEAFKTLCRHEGIIPALESSHALAHALKMMREQPEKEQLLVVNLSGRGDKDIFTVHDILKARG 395
                                    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       331       341       351       361       371       381       391    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit

(-) CATH Domains  (2, 3)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit

(-) Gene Ontology  (12, 21)

Asymmetric Unit(hide GO term definitions)
Chain A   (TRPA_SALTY | P00929)
molecular function
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0004834    tryptophan synthase activity    Catalysis of the reaction: L-serine + (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H2O.
biological process
    GO:0009073    aromatic amino acid family biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    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: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.
    GO:0000162    tryptophan biosynthetic process    The chemical reactions and pathways resulting in the formation of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; tryptophan is synthesized from chorismate via anthranilate.
    GO:0006568    tryptophan metabolic process    The chemical reactions and pathways involving tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain B   (TRPB_SALTY | P0A2K1)
molecular function
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0004834    tryptophan synthase activity    Catalysis of the reaction: L-serine + (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H2O.
biological process
    GO:0009073    aromatic amino acid family biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    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:0000162    tryptophan biosynthetic process    The chemical reactions and pathways resulting in the formation of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; tryptophan is synthesized from chorismate via anthranilate.
    GO:0006568    tryptophan metabolic process    The chemical reactions and pathways involving tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TRPA_SALTY | P009291a50 1a5a 1a5b 1a5s 1beu 1bks 1c29 1c8v 1c9d 1cw2 1cx9 1fuy 1k3u 1k7e 1k7f 1k7x 1k8x 1k8y 1kfb 1kfc 1kfe 1kfj 1kfk 1qop 1qoq 1tjp 1ttp 1ttq 1ubs 1wbj 2cle 2clf 2clh 2cli 2clk 2cll 2clm 2clo 2j9x 2j9y 2j9z 2rh9 2rhg 2trs 2tsy 2tys 2wsy 3cep 3pr2 4hn4 4hpj 4hpx 4ht3 4kkx 4wx2 4xug 4y6g 4zqc 5bw6 5cgq
        TRPB_SALTY | P0A2K11a50 1a5a 1a5b 1a5s 1beu 1bks 1c29 1c8v 1c9d 1cw2 1cx9 1fuy 1k3u 1k7e 1k7f 1k7x 1k8x 1k8y 1kfb 1kfc 1kfe 1kfj 1kfk 1qop 1qoq 1tjp 1ttp 1ttq 1ubs 1wbj 2cle 2clf 2clh 2cli 2clk 2cll 2clm 2clo 2j9x 2j9y 2j9z 2rh9 2rhg 2trs 2tsy 2tys 2wsy 3cep 3pr2 4hn4 4hpj 4hpx 4ht3 4kkx 4wx2 4xug 4y6g 4zqc 5bw6 5cgq

(-) Related Entries Specified in the PDB File

1k7x CRYSTAL STRUCTURE OF THE BETA-SER178PRO MUTANT OF TRYPTOPHAN SYNTHASE
1k8y CRYSTAL STRUCTURE OF THE TRYPTOPHAN SYNTHASE BETA-SER178PRO MUTANT COMPLEXED WITH D,L-ALPHA-GLYCEROL-3-PHOSPHATE