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 CRYSTAL STRUCTURE OF HUMAN EEFSEC IN COMPLEX WITH GDPNP
 
Authors :  M. Dobosz-Bartoszek, Z. Otwinowski, M. Simonovic
Date :  25 Mar 16  (Deposition) - 12 Oct 16  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Elongation Factor, Selenocysteine, Selenocysteine Trna, Translation, Gtpase, Gdpnp, Gtp (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Dobosz-Bartoszek, M. H. Pinkerton, Z. Otwinowski, S. Chakravarthy, D. Soll, P. R. Copeland, M. Simonovic
Crystal Structures Of The Human Elongation Factor Eefsec Suggest A Non-Canonical Mechanism For Selenocysteine Incorporation.
Nat Commun V. 7 12941 2016
PubMed-ID: 27708257  |  Reference-DOI: 10.1038/NCOMMS12941

(-) Compounds

Molecule 1 - SELENOCYSTEINE-SPECIFIC ELONGATION FACTOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: EEFSEC, SELB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ELONGATION FACTOR SEC,EUKARYOTIC ELONGATION FACTOR, SELENOCYSTEINE-TRNA-SPECIFIC

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 33)

Asymmetric Unit (3, 33)
No.NameCountTypeFull Name
1GNP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MN2Ligand/IonMANGANESE (II) ION
3MSE29Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 15)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MN-1Ligand/IonMANGANESE (II) ION
3MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 16)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MN-1Ligand/IonMANGANESE (II) ION
3MSE15Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:21 , THR A:48 , GNP A:1002binding site for residue MN A 1001
2AC2SOFTWAREILE A:16 , ASP A:17 , GLY A:19 , LYS A:20 , THR A:21 , ALA A:22 , ILE A:47 , THR A:48 , ASN A:146 , LYS A:147 , ASP A:149 , LEU A:150 , ALA A:185 , ALA A:186 , LYS A:187 , GLY A:189 , GLY A:190 , MN A:1001binding site for residue GNP A 1002
3AC3SOFTWARETHR B:21 , THR B:48 , GNP B:1002binding site for residue MN B 1001
4AC4SOFTWAREILE B:16 , SER B:18 , GLY B:19 , LYS B:20 , THR B:21 , ALA B:22 , THR B:48 , GLY B:95 , ASN B:146 , LYS B:147 , ASP B:149 , ALA B:186 , LYS B:187 , MN B:1001binding site for residue GNP B 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IZM)

(-) 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:460
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee....hhhhhhhhhhhh......eeeeeeee.hhhhhh..eeeeeeee...hhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhhhhhh.......eee..........hhhhhhhhhhhhh...........eeeeeeee...eeeeeeeee..ee...........................ee....ee..ee..........eeee.......eeeeeee.ee.............eeee....eeeee..eeee...................eee..........eeeeeeeeee......eeeee............eeeeee..eee...hhhhhhhhhh.ee.......................................................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5izm A   3 GRRVNVNVGVLGHIDSGKTALARALSTTAITLDLGFSCFSVPLPARLRSSPLLQVTLVDCPGHASLIRTIIGGAQIIDLmmLVIDVTKGmQTQSAECLVIGQIACQKLVVVLNKIDLLPEGKRQAAIDKmTKKmQKTLENTKFRGAPIIPVAAKPGGAPQGIPELIELLTSQISIPTRDPSGPFLmSVDHCFSIGTVmTGTILSGSISLGDSVEIPALKVVKKVKSmQmFHmPITSAmQGDRLGICVTQFDPKLLERGLVCAPESLHTVHAALISVEKIPYFRGPLQTKAKFHITVGHETVmGRLmFFSPAPDNFDQEPILDSFNFSQEYLFQEQYLSPRQQWALVEFEKPVTCPRLCLVIGSRLDADIHTNTCRLAFHGILLHGLEDRNYADSFLPRLKVYKLKHKDDYSVQLFVGLKVHLSTGELGIIDSFKIHIPGGLLSLTFKRYVFDTHKRmVQS 595
                                    12        22        47        57        67|       93       103       113|      123       133       143       153       163   |   173       183      |200       210       220     | 230   ||  243       253       263      |273 |     283       293       303       313       323       333       343 |   | 353       363       373       408       418       428       438       448       458       468      |486 ||    508       518 ||    535||     585      |595
                                                       31|                  67|                          113-MSE   123-MSE                                 163-MSE                    190|                         226-MSE 234|  |                          270-MSE|     |                                                             345-MSE                             381|                                                                 475| 488|                520|     536|            592-MSE
                                                        47                   84                           114-MSE                                              167-MSE                 198                                  238  |                            272-MSE    |                                                                 349-MSE                          407                                                                  484  501                 528      577                  
                                                                                                                                                                                                                               241-MSE                           275-MSE |                                                                                                                                                                                                                              
                                                                                                                                                                                                                                                                       281-MSE                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:495
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeee....hhhhhhhhhhhhh......eeeeeeee.hhhhh.....eeeeeeee...hhhhhhhhhhh.....eeeeeee.....hhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhh.........eee..........hhhhhhhhhhhh...........eeeeeeee......eeeeeeeee.eee...eeee....eeee..eeee..ee..eee.....eeee...hhhhh...eee.....eeeeeeeeeeee............eeeeee..eeeeeeeeeeee...................eee..........eeeeeeeeeeee....eeee.............eeeeeeeee...hhhhhhhhhh.eee..eee.ee..........ee.....hhhhhh..eeee...eeeee........ee.....hhhhhhhh...eeee..ee............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5izm B   4 RRVNVNVGVLGHIDSGKTALARALSTTAGITLDLGFSCFSVPLPARLRSSLEPLLQVTLVDCPGHASLIRTIIGGAQIIDLmmLVIDVTKGmQTQSAECLVIGQIACQKLVVVLNKIDLLPERQAAIDKmTKKmQKTLENTKFRGAPIIPVAAKPGGPQGIPELIELLTSQISIPTRDPSGPFLmSVDHCFSIKGQGTVmTGTILSGSISLGDSVEIPALKVVKKVKSmQmFHmPITSAmQGDRLGICVTQFDPKLLERGLVCAPESLHTVHAALISVEKIPYFRGPLQTKAKFHITVGHETVmGRLmFFSPAPDNFDQEPILDSFNFSQEYLFQEQYLSPRQQWALVEFEKPVTCPRLCLVIGSRLDAHTNTCRLAFHGILLHGLEDRNYADSFLPRLKVYKLKHKHGLVERAmDDYSVIGRSLFETNIQLFVGLKVHLSTGELGIIDSAFGKFKIHIPGGLSPESKKILSQHVVLSLTFKRYVFDTHKRmVQS 595
                                    13        23       |47        57        67||      91       101       111 ||    121 |     131       141       151 ||    163   |   173       183      |201       211       221    |  231       241       251       261       271|  |   281       291       301       311       321       331       341   |   351       361       371       381|      416       426       438       448       458       468       478    |  488     ||500       510       520  ||   533       543||     580       590 |   
                                                      31|                    68|                           113-MSE   123-MSE                       153|      |   |                    190|                        226-MSE        241-MSE                      270-MSE|     |                                                             345-MSE                             381|                         435|                                          483-MSE    494|                       523|              544|                 592-MSE
                                                       46                     83                            114-MSE                                 156      |   |                     199                                                                      272-MSE    |                                                                 349-MSE                          407                          438                                                      497                        527               572                       
                                                                                                                                                           163-MSE                                                                                                 275-MSE |                                                                                                                                                                                                                                                               
                                                                                                                                                               167-MSE                                                                                                   281-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 5IZM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

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
    GNP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5izm)
 
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
  5izm
    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
  SELB_HUMAN | P57772
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  SELB_HUMAN | P57772
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SELB_HUMAN | P57772: 5izk 5izl

(-) Related Entries Specified in the PDB File

5izk 5izl