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 :  CRYSTAL STRUCTURE OF MCCF-LIKE PROTEIN (BA_5613) IN THE COMPLEX WITH ASPARTYL SULFAMOYL ADENYLATE
 
Authors :  B. Nocek, W. F. Anderson, A. Joachimiak, Center For Structural Geno Infectious Diseases (Csgid)
Date :  13 Feb 17  (Deposition) - 15 Mar 17  (Release) - 15 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Hydrolase, S66, Mccf-Like Protein, Microcin C, Aspartyl Sulfamoyl Adenylate, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, W. F. Anderson, A. Joachimiak
Crystal Structure Of Mccf-Like Protein (Ba_5613) In The Complex With Aspartyl Sulfamoyl Adenylate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEPTIDASE S66
    Chains: A, B, C, D
    Engineered: YES
    Expression System: BACILLUS ANTHRACIS STR. AMES
    Expression System Taxid: 198094
    Gene: YOCD, GBAA_5613, A8C77_27310, BASH2_00378
    Organism Scientific: BACILLUS ANTHRACIS
    Organism Taxid: 1392
    Synonym: PUTATIVE CARBOXYPEPTIDASE YOCD

 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  (3, 34)

Asymmetric Unit (3, 34)
No.NameCountTypeFull Name
1DSZ4Ligand/Ion5'-O-(L-ALPHA-ASPARTYLSULFAMOYL)ADENOSINE
2GOL2Ligand/IonGLYCEROL
3MSE28Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 17)
No.NameCountTypeFull Name
1DSZ2Ligand/Ion5'-O-(L-ALPHA-ASPARTYLSULFAMOYL)ADENOSINE
2GOL1Ligand/IonGLYCEROL
3MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (3, 17)
No.NameCountTypeFull Name
1DSZ2Ligand/Ion5'-O-(L-ALPHA-ASPARTYLSULFAMOYL)ADENOSINE
2GOL1Ligand/IonGLYCEROL
3MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:19 , ILE A:23 , LEU A:83 , GLY A:84 , GLY A:85 , TYR A:86 , TYR A:110 , SER A:111 , HIS A:133 , TRP A:173 , TYR A:174 , HIS A:299 , HOH A:501 , HOH A:503 , HOH A:505 , HOH A:513 , HOH A:531 , HOH A:560 , HOH A:574 , HOH A:587 , HOH A:601 , HOH A:622 , HOH A:637binding site for residue DSZ A 401
2AC2SOFTWAREGLY A:142 , GLU A:144 , TYR A:145 , GLU A:166 , THR A:167 , PRO A:302 , HOH A:581 , HOH A:664binding site for residue GOL A 402
3AC3SOFTWAREILE B:23 , LEU B:83 , GLY B:84 , GLY B:85 , TYR B:86 , TYR B:110 , SER B:111 , HIS B:133 , TRP B:173 , TYR B:174 , HIS B:299 , HOH B:601 , HOH B:602 , HOH B:604 , HOH B:605 , HOH B:611 , HOH B:625 , HOH B:631 , HOH B:653 , HOH B:664 , HOH B:665 , HOH B:688 , HOH B:700binding site for residue DSZ B 500
4AC4SOFTWARECYS C:19 , ILE C:23 , LEU C:83 , GLY C:84 , GLY C:85 , TYR C:86 , TYR C:110 , SER C:111 , HIS C:133 , TYR C:174 , HIS C:299 , HOH C:515 , HOH C:517 , HOH C:522 , HOH C:527 , HOH C:542 , HOH C:545 , HOH C:570binding site for residue DSZ C 401
5AC5SOFTWAREGLY C:142 , LEU C:143 , GLU C:144 , TYR C:145 , THR C:167binding site for residue GOL C 402
6AC6SOFTWARECYS D:19 , ILE D:23 , LEU D:83 , GLY D:84 , GLY D:85 , TYR D:86 , TYR D:110 , SER D:111 , HIS D:133 , TRP D:173 , TYR D:174 , HIS D:299 , HOH D:601 , HOH D:606 , HOH D:611 , HOH D:624 , HOH D:625binding site for residue DSZ D 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Thr A:301 -Pro A:302
2Thr B:301 -Pro B:302
3Thr C:301 -Pro C:302
4Thr D:301 -Pro D:302

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5USD)

(-) 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:329
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee....hhhhhhhhhhhhhhhhhhhh..eeee.............hhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhh..eee...hhhhhh...hhhhhhhhhhhhhh...eee....ee..............ee....eeee.eeeeeeeeeeehhhhhh............eeeeee....hhhhhhhhhhhhhhhhhh..hhhhh.eeeee..hhhhh.hhhhhhhhhhhhhhhh...eeeee..........eee..eeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5usd A   0 AmLPTKLKKGDEIRVISPSCSLSIVSTENRRLAVKRLTELGFHVTFSTHAEEIDRFASSSISSRVQDLHEAFRDPNVKAILTTLGGYNSNGLLKYLDYDLIRENPKFFCGYSDITALNNAIYTKTGLVTYSGPHFSSFGmEKGLEYTTDYFLQCLTSNKPIEVLPSETWSDDSWYIDQENRKFIKNEGYVSIHEGEATGDIIGGNmSTLNLLQGTSYmPNLKDKILFLEEDSLTGTSTLKTFDRYLHSLmQQQNFKHVKGIVIGKmQKGAECTIEDIQEmIASKPELAHIPIIANASFGHTTPIFTFPIGGRATIISSKEKTSITILTH 328
                             |       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       299       309       319         
                             |                                                                                                                                       139-MSE                                                           205-MSE     217-MSE                         249-MSE         265-MSE       279-MSE                                             
                             1-MSE                                                                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:330
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eeeee....hhhhhhhhhhhhhhhhhhhh..eeee.............hhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhh..eee..hhhhhhh...hhhhhhhhhhhhhh...eee....ee..............ee....eeee.eeeeeeeeeeehhhhhh............eeeeee....hhhhhhhhhhhhhhhhhh..hhhhh.eeeee..hhhhh.hhhhhhhhhhhhhhhh...eeeee..........eee..eeeeee.....eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5usd B  -1 NAmLPTKLKKGDEIRVISPSCSLSIVSTENRRLAVKRLTELGFHVTFSTHAEEIDRFASSSISSRVQDLHEAFRDPNVKAILTTLGGYNSNGLLKYLDYDLIRENPKFFCGYSDITALNNAIYTKTGLVTYSGPHFSSFGmEKGLEYTTDYFLQCLTSNKPIEVLPSETWSDDSWYIDQENRKFIKNEGYVSIHEGEATGDIIGGNmSTLNLLQGTSYmPNLKDKILFLEEDSLTGTSTLKTFDRYLHSLmQQQNFKHVKGIVIGKmQKGAECTIEDIQEmIASKPELAHIPIIANASFGHTTPIFTFPIGGRATIISSKEKTSITILTH 328
                              |      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       298       308       318       328
                              1-MSE                                                                                                                                   139-MSE                                                           205-MSE     217-MSE                         249-MSE         265-MSE       279-MSE                                             


Chain C from PDB  Type:PROTEIN  Length:329
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee....hhhhhhhhhhhhhhhhhhhh..eeee.............hhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhh..eee...hhhhhh...hhhhhhhhhhhhhh...eee....ee..............ee....eeee.eeeeeeeeeeehhhhhh............eeeeee....hhhhhhhhhhhhhhhhhh..hhhhh.eeeeee.hhhhh.hhhhhhhhhhhhhhhh...eeeeeeee.......eee..eeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5usd C   0 AmLPTKLKKGDEIRVISPSCSLSIVSTENRRLAVKRLTELGFHVTFSTHAEEIDRFASSSISSRVQDLHEAFRDPNVKAILTTLGGYNSNGLLKYLDYDLIRENPKFFCGYSDITALNNAIYTKTGLVTYSGPHFSSFGmEKGLEYTTDYFLQCLTSNKPIEVLPSETWSDDSWYIDQENRKFIKNEGYVSIHEGEATGDIIGGNmSTLNLLQGTSYmPNLKDKILFLEEDSLTGTSTLKTFDRYLHSLmQQQNFKHVKGIVIGKmQKGAECTIEDIQEmIASKPELAHIPIIANASFGHTTPIFTFPIGGRATIISSKEKTSITILTH 328
                             |       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       299       309       319         
                             1-MSE                                                                                                                                   139-MSE                                                           205-MSE     217-MSE                         249-MSE         265-MSE       279-MSE                                             


Chain D from PDB  Type:PROTEIN  Length:330
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eeeee....hhhhhhhhhhhhhhhhhhhh..eeee.............hhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhh..ee..hhhhhhhhhhhhhhhh..eee...hhhhhh...hhhhhhhhhhhhhh...eee....ee..............ee....eeee.eeeeeeeeeeehhhhhh............eeeeee....hhhhhhhhhhhhhhhhhh..hhhhh.eeeeee.hhhhh.hhhhhhhhhhhhhhhh...eeeeeeee.......eee..eeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5usd D  -1 NAmLPTKLKKGDEIRVISPSCSLSIVSTENRRLAVKRLTELGFHVTFSTHAEEIDRFASSSISSRVQDLHEAFRDPNVKAILTTLGGYNSNGLLKYLDYDLIRENPKFFCGYSDITALNNAIYTKTGLVTYSGPHFSSFGmEKGLEYTTDYFLQCLTSNKPIEVLPSETWSDDSWYIDQENRKFIKNEGYVSIHEGEATGDIIGGNmSTLNLLQGTSYmPNLKDKILFLEEDSLTGTSTLKTFDRYLHSLmQQQNFKHVKGIVIGKmQKGAECTIEDIQEmIASKPELAHIPIIANASFGHTTPIFTFPIGGRATIISSKEKTSITILTH 328
                              |      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       298       308       318       328
                              1-MSE                                                                                                                                   139-MSE                                                           205-MSE     217-MSE                         249-MSE         265-MSE       279-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 5USD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
    DSZ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ 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 ]
 
  Cis Peptide Bonds
    Thr A:301 - Pro A:302   [ RasMol ]  
    Thr B:301 - Pro B:302   [ RasMol ]  
    Thr C:301 - Pro C:302   [ RasMol ]  
    Thr D:301 - Pro D:302   [ 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
  5usd
    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
  Q81JT5_BACAN | Q81JT5
    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)
  (no 'Enzyme Classificator' available)
    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
  Q81JT5_BACAN | Q81JT5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q81JT5_BACAN | Q81JT5: 4e5s 5fd8

(-) Related Entries Specified in the PDB File

4e5s
5fd8 RELATED ID: CSGID-IDP91764 RELATED DB: TARGETTRACK