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

(-) Description

Title :  THE STRUCTURE OF CYSTEINE SYNTHASE FROM MYCOBACTERIUM ULCERANS AGY99
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  21 Nov 12  (Deposition) - 26 Dec 12  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Ssgcid, Seattle Structural Genomics Center For Infectious Disease, Cysteine Synthase, Niaid, National Institute Of Allergy And Infectious Diseases, Synthase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, I. Phan, D. W. Begley, M. C. Clifton, B. Armour, D. M. Dranow, B. M. Taylor, M. M. Muruthi, J. Abendroth, J. W. Fairman, D. Fox, S. H. Dieterich, B. L. Staker, A. S. Gardberg, R. Choi, S. N. Hewitt, A. J. Napuli, J. Myers, L. K. Barrett, Y. Zhang, M. Ferrell, E. Mundt, K. Thompkins, N. Tran, S. Lyons-Abbott, A. Abramov, A. Sekar, D. Serbzhinskiy, D. Lorimer, G. W. Buchko, R. Stacy, L. J. Stewart, T. E. Edwards, W. C. Van Voorhis, P. J. Myler
Increasing The Structural Coverage Of Tuberculosis Drug Targets.
Tuberculosis (Edinb) V. 95 142 2015
PubMed-ID: 25613812  |  Reference-DOI: 10.1016/J.TUBE.2014.12.003

(-) Compounds

Molecule 1 - CYSTEINE SYNTHASE
    Chains: A, B, C, D
    EC Number: 2.5.1.47
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CYSK1, MUL_1465
    Organism Scientific: MYCOBACTERIUM ULCERANS
    Organism Taxid: 362242
    Strain: AGY99

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:71 , SER A:72 , GLY A:73 , ASN A:74 , THR A:75BINDING SITE FOR RESIDUE SO4 A 402
2AC2SOFTWAREARG B:18 , ASP B:29BINDING SITE FOR RESIDUE CL B 401
3AC3SOFTWARELYS B:169 , ARG B:194BINDING SITE FOR RESIDUE SO4 B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I1Y)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Gly A:25 -Ala A:26
2Leu A:292 -Pro A:293
3Gly B:25 -Ala B:26
4Leu B:292 -Pro B:293
5Gly C:25 -Ala C:26
6Leu C:292 -Pro C:293
7Gly D:25 -Ala D:26
8Leu D:292 -Pro D:293

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I1Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I1Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4I1Y)

(-) 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:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains d4i1ya_ A: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhh....eee..........eeeeee.hhh....hhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhh..ee.....hhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhh...eeeeee.......eeee...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i1y A   1 MTIAENIAQLIGGTPLVRLRRVTDGAAADVVAKLESFNPAGSIKDRIGVAMIDAAEKAGLIKPDTIILEPTSGNTGIALAMVSAARGYKCVLTMPDTMSIERRMLLRAYGAELVLTPGAEGMAGAIAKAEELAKTDDRYFIPQNPAVHAVTTAEEVWRDTDGKVDIFVSGVGTGGTITGVAQVIKQRRPSAQFVAVEPDLALVDEVITVGNDDALELARRMATEEGLLFGISSGAAVWAARELAHRPENAGKLIVVVLPDFGE 297
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  ||   156       166       176       186       196       234       244       254       264       274       284       294   
                                                                                                                                                                        143|                                                   204|                                                                
                                                                                                                                                                         150                                                    233                                                                


Chain B from PDB  Type:PROTEIN  Length:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains d4i1yb_ B: automated matches                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee.hhhhhh....eee..........eeeeee.hhh....hhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhh..ee.....hhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhh...eeeeeee........eeeee..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4i1y B   0 SMTIAENIAQLIGGTPLVRLRRVTDGAAADVVAKLESFNPAGSIKDRIGVAMIDAAEKAGLIKPDTIILEPTNTGIALAMVSAARGYKCVLTMPDTMSIERRMLLRAYGAELVLTPGAEGMAGAIAKAEELAKTDDRYFIPQNPAVHAVTTAEEVWRDTDGKVDIFVSGVGTGGTITGVAQVIKQRRPSAQFVAVEPALDLALVDEVITVGNDDALELARRMATEEGLLFGISSGAAVWAARELAHRPENAGKLIVVVLPDFGE 297
                                     9        19        29        39        49        59        69 ||     81        91       101       111       121       131       141 ||    157       167       177       187       197       233       243       253       263       273       283       293    
                                                                                                  71|                                                                  143|                                                    205|                                                                 
                                                                                                   74                                                                   150                                                     232                                                                 


Chain C from PDB  Type:PROTEIN  Length:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains d4i1yc_ C: automated matches                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.hhhhhh....eee..........eeeeee.hhh....hhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhh..ee....hhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhh...eeeeee..........eeee...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i1y C  -2 PGSMTIAENIAQLIGGTPLVRLRRVTDGAAADVVAKLESFNPAGSIKDRIGVAMIDAAEKAGLIKPDTIILEPTSGNTGIALAMVSAARGYKCVLTMPDTMSIERRMLLRAYGAELVLTPGAEGMAGAIAKAEELAKTDDRYFIPNPAVHAVTTAEEVWRDTDGKVDIFVSGVGTGGTITGVAQVIKQRRPSAQFVAVEPPVLDLALVDEVITVGNDDALELARRMATEEGLLFGISSGAAVWAARELAHRPENAGKLIVVVLPDFGE 297
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137    || 154       164       174       184       194       204|      239       249       259       269       279       289        
                                                                                                                                                                          142|                                                   204|                                                                   
                                                                                                                                                                           150                                                    230                                                                   


Chain D from PDB  Type:PROTEIN  Length:270
                                                                                                                                                                                                                                                                                                              
               SCOP domains d4i1yd_ D: automated matches                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee.hhhhhh....eee..........eeeeee.hhh....hhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh..ee....hhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhh...eeeeeee..............eeeee...hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4i1y D  -1 GSMTIAENIAQLIGGTPLVRLRRVTDGAAADVVAKLESFNPAGSIKDRIGVAMIDAAEKAGLIKPDTIILEPTTGIALAMVSAARGYKCVLTMPDTMSIERRMLLRAYGAELVLTPGAEGMAGAIAKAEELAKTDDRYFIPNPAVHAVTTAEEVWRDTDGKVDIFVSGVGTGGTITGVAQVIKQRRPSAQFVAVEPAGFVPPVLDLALVDEVITVGNDDALELARRMATEEGLLFGISSGAAVWAARELAHRPENAGKLIVVVLPDFGER 298
                                     8        18        28        38        48        58        68  ||    81        91       101       111       121       131       141||     158       168       178       188       198      |228       238       248       258       268       278       288       298
                                                                                                   71|                                                                142|                                                    205|                                                                        
                                                                                                    75                                                                 150                                                     226
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I1Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I1Y)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:25 - Ala A:26   [ RasMol ]  
    Gly B:25 - Ala B:26   [ RasMol ]  
    Gly C:25 - Ala C:26   [ RasMol ]  
    Gly D:25 - Ala D:26   [ RasMol ]  
    Leu A:292 - Pro A:293   [ RasMol ]  
    Leu B:292 - Pro B:293   [ RasMol ]  
    Leu C:292 - Pro C:293   [ RasMol ]  
    Leu D:292 - Pro D:293   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  4i1y
    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
  A0PNS1_MYCUA | A0PNS1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  2.5.1.47
    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
  A0PNS1_MYCUA | A0PNS1
    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 4I1Y)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4I1Y)