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 OXIDOREDUCTASE, GFO/IDH/MOCA FAMILY FROM STREPTOCOCCUS PNEUMONIAE WITH REDUCTIVE METHYLATED LYSINE
 
Authors :  C. Chang, C. Hatzos-Skintges, J. Abdullah, A. Joachimiak, Midwest Ce Structural Genomics (Mcsg)
Date :  10 Jan 13  (Deposition) - 23 Jan 13  (Release) - 23 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Structural Genomics, Midwest Center For Structural Genomics, Psi- Biology, Mcsg, Oxidoreductase, Gfo/Idh/Moca Family, Reductive Methylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chang, C. Hatzos-Skintges, J. Abdullah, A. Joachimiak
Crystal Structure Of Oxidoreductase, Gfo/Idh/Moca Family From Streptococcus Pneumoniae With Reductive Methylated Lysine
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - OXIDOREDUCTASE, GFO/IDH/MOCA FAMILY
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PMCSG7
    Gene: SP_1482
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313

 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  (3, 33)

Asymmetric Unit (3, 33)
No.NameCountTypeFull Name
1K5Ligand/IonPOTASSIUM ION
2MLY8Mod. Amino AcidN-DIMETHYL-LYSINE
3MSE20Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 14)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2MLY4Mod. Amino AcidN-DIMETHYL-LYSINE
3MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 14)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2MLY4Mod. Amino AcidN-DIMETHYL-LYSINE
3MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:56 , ALA B:81 , HOH B:622 , HOH B:708BINDING SITE FOR RESIDUE K B 401
2AC2SOFTWARELYS B:192 , SER B:305 , GLU B:308 , HOH B:620 , HOH B:663BINDING SITE FOR RESIDUE K B 402
3AC3SOFTWARELEU C:234 , ASN C:248 , THR C:249 , HOH C:604 , HOH C:613BINDING SITE FOR RESIDUE K C 401
4AC4SOFTWARELEU D:234 , ASN D:248 , HOH D:593 , HOH D:610BINDING SITE FOR RESIDUE K D 401
5AC5SOFTWAREASN B:233 , GLU D:237 , THR D:246 , HOH D:595BINDING SITE FOR RESIDUE K D 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IQ0)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:93 -Pro A:94
2Lys B:93 -Pro B:94
3Lys C:93 -Pro C:94
4Lys D:93 -Pro D:94

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IQ0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IQ0)

(-) Exons   (0, 0)

(no "Exon" information available for 4IQ0)

(-) 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:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.....eee.hhhhhhh....eeee..hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh...eeeeeeeee.......hhhhhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeeeee....eeeeeee........eeeee..eeeee........eeeee....eee.........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iq0 A  -1 NAmLKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKLETAATFASRYQNIQLFDQLEVFFKSSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIkNFLADkQVLGADFNYAKYSSKAGGALmDLGIYPLYAAVRLFGKANDATYHAQQLDNSIDLNGDGILFYPDYQVHIKAGKNITSNLPCEIYTTDGTLTLNTIEHIRSAIFTDHQGNQVQLPIQQAPHTmTEEVAAFAHmIQQPDLNLYQTWLYDAGSVHELLYTmRQTAGIRFE 322
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128   |   138       148    || 175|      185       195       205       215       225       235       245       255       265       275 |     285 |     295       305       315       
                              |                                                                                                                                132-MLY |            153|    |                                                                                                  277-MSE   287-MSE                   313-MSE     
                              1-MSE                                                                                                                                  138-MLY         171    |                                                                                                                                                  
                                                                                                                                                                                          176-MSE                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.....eee.hhhhhhh....eeee..hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh...eeeeeeeee........hhhhhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeeeee....eeeeeee........eeeee..eeeee........eeeee....eee.........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4iq0 B   0 AmLKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKLETAATFASRYQNIQLFDQLEVFFKSSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIkNFLADkQVLGADFNYAKYSSRFAGGALmDLGIYPLYAAVRLFGKANDATYHAQQLDNSIDLNGDGILFYPDYQVHIKAGKNITSNLPCEIYTTDGTLTLNTIEHIRSAIFTDHQGNQVQLPIQQAPHTmTEEVAAFAHmIQQPDLNLYQTWLYDAGSVHELLYTmRQTAGIRF 321
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129  |    139       149  ||   175|      185       195       205       215       225       235       245       255       265       275 |     285 |     295       305       315      
                             1-MSE                                                                                                                            132-MLY |           152|      |                                                                                                  277-MSE   287-MSE                   313-MSE    
                                                                                                                                                                    138-MLY        169      |                                                                                                                                                 
                                                                                                                                                                                          176-MSE                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.....eee.hhhhhh.....eeee..hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh...eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeeeee....eeeeeee........eeeee..eeeee........eeeee....eee.........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iq0 C   1 mLKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKLETAATFASRYQNIQLFDQLEVFFKSSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIkNFLADkQVLGADFNYAKYSSVFSDRFAGGALmDLGIYPLYAAVRLFGKANDATYHAQQLDNSIDLNGDGILFYPDYQVHIKAGKNITSNLPCEIYTTDGTLTLNTIEHIRSAIFTDHQGNQVQLPIQQAPHTmTEEVAAFAHmIQQPDLNLYQTWLYDAGSVHELLYTmRQTAGIR 320
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130 |     140       150 ||    172   |   182       192       202       212       222       232       242       252       262       272    |  282    |  292       302       312|       
                            1-MSE                                                                                                                            132-MLY |           152|        176-MSE                                                                                              277-MSE   287-MSE                   313-MSE   
                                                                                                                                                                   138-MLY        165                                                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:310
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.....eee.hhhhhhhh...eeee..hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh...eeeeeeeee......hhhhh.hhhhhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeeeee....eeeeeee........eeeee..eeeee........eeeee....eee.........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iq0 D   0 AmLKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKLETAATFASRYQNIQLFDQLEVFFKSSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIkNFLADkQVLGADFNYAKYSSKFSDRFAGGALmDLGIYPLYAAVRLFGKANDATYHAQQLDNSIDLNGDGILFYPDYQVHIKAGKNITSNLPCEIYTTDGTLTLNTIEHIRSAIFTDHQGNQVQLPIQQAPHTmTEEVAAFAHmIQQPDLNLYQTWLYDAGSVHELLYTmRQTAGIRF 321
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129  |    139       149   ||  171    |  181       191       201       211       221       231       241       251       261       271     | 281     | 291       301       311 |     321
                             1-MSE                                                                                                                            132-MLY |            153|       176-MSE                                                                                              277-MSE   287-MSE                   313-MSE    
                                                                                                                                                                    138-MLY         166
   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 4IQ0)

(-) CATH Domains  (0, 0 ; only for superseded entry 2HO3: 2,8)

(no "CATH Domain" information available for 4IQ0, only for superseded entry 2HO3 replaced by 4IQ0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IQ0)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4IQ0)

 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
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MLY  [ 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 ]
 
  Cis Peptide Bonds
    Lys A:93 - Pro A:94   [ RasMol ]  
    Lys B:93 - Pro B:94   [ RasMol ]  
    Lys C:93 - Pro C:94   [ RasMol ]  
    Lys D:93 - Pro D:94   [ 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
  4iq0
    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
  A0A0H2UR04_S | A0A0H2UR04
    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
  A0A0H2UR04_S | A0A0H2UR04
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A0A0H2UR04_S | A0A0H2UR04: 2ho5 4nhe

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4IQ0)