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 :  STRUCTURE OF HOMO SAPIENS ACETYLCHOLINESTERASE PHOSPHONYLATED BY SARIN.
 
Authors :  A. Allgardsson, L. Berg, C. Akfur, A. Hornberg, F. Worek, A. Linusson, F
Date :  02 Dec 15  (Deposition) - 11 May 16  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (1x),B (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Hydrolase, Signaling Protein, Acetylcholinesterase, Sarin, Hi-6, Qm, Density Functional Theory Calculations, Michaelis Complex. (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Allgardsson, L. Berg, C. Akfur, A. Hornberg, F. Worek, A. Linusson, F. J. Ekstrom
Structure Of A Prereaction Complex Between The Nerve Agent Sarin, Its Biological Target Acetylcholinesterase, And The Antidote Hi-6.
Proc. Natl. Acad. Sci. Usa V. 113 5514 2016
PubMed-ID: 27140636  |  Reference-DOI: 10.1073/PNAS.1523362113

(-) Compounds

Molecule 1 - ACETYLCHOLINESTERASE
    Chains: A, B
    EC Number: 3.1.1.7
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: CATALYTIC DOMAIN, UNP RESIDUES 33-574
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ACHE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2SGB2Mod. Amino AcidO-[(S)-METHYL(1-METHYLETHOXY)PHOSPHORYL]-L-SERINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2SGB1Mod. Amino AcidO-[(S)-METHYL(1-METHYLETHOXY)PHOSPHORYL]-L-SERINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
2SGB1Mod. Amino AcidO-[(S)-METHYL(1-METHYLETHOXY)PHOSPHORYL]-L-SERINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:241 , ASP A:304 , GLY A:305 , ASP A:306 , HOH A:2041 , ASN B:283BINDING SITE FOR RESIDUE 1PE A1543

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:69 -A:96
2A:257 -A:272
3A:409 -A:529
4B:69 -B:96
5B:257 -B:272
6B:409 -B:529

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:105 -Pro A:106
2Tyr B:105 -Pro B:106

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FPQ)

(-) 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:532
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhh.eeee..eeee.eee......eeeeeeee.....hhhhh............eee......ee..........hhhhhh......ee....eeeeeee.......eeeeeee...........hhhhhhhhhhhhhh.eeeee...hhhhhhh..........hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee..hhhhhhhhhhhhhhhhh...eeeee...........hhhhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhh.....................hhhhhhhhh.....eeeeeee...hhhhhh..............hhhhhhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhh.....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..................eeeee.....eeee..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fpq A   4 EDAELLVTVRGGRLRGIRLKTPGGPVSAFLGIPFAEPPMGPRRFLPPEPKQPWSGVVDATTFQSVCYQYVDTLYPGFEGTEMWNPNRELSEDCLYLNVWTPYPRPTSPTPVLVWIYGGGFYSGASSLDVYDGRFLVQAERTVLVSMNYRVGAFGFLALPGSREAPGNVGLLDQRLALQWVQENVAAFGGDPTSVTLFGEsAGAASVGMHLLSPPSRGLFHRAVLQSGAPNGPWATVGMGEARRRATQLAHLVGCPGGNDTELVACLRTRPAQVLVNHEWHVLPQESVFRFSFVPVVDGDFLSDTPEALINAGDFHGLQVLVGVVKDEGSYFLVYGAPGFSKDNESLISRAEFLAGVRVGVPQVSDLAAEAVVLHYTDWLHPEDPARLREALSDVVGDHNVVCPVAQLAGRLAAQGARVYAYVFEHRASTLSWPLWMGVPHGYEIEFIFGIPLDPSRNYTAEEKIFAQRLMRYWANFARTGDPNEPRDPQWPPYTAGAQQYVSLDLRPLEVRRGLRAQACAFWNRFLPKLLSA 542
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253    || 267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487      |500       510       520       530       540  
                                                                                                                                                                                                                                 203-SGB                                                258|                                                                                                                                                                                                                                    494|                                            
                                                                                                                                                                                                                                                                                         263                                                                                                                                                                                                                                     498                                            


Chain B from PDB  Type:PROTEIN  Length:530
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhh.eeee..eeee.eee......eeeeeeee.....hhhhh............eee......ee..........hhhhhh......ee....eeeeeee.......eeeeeee...........hhhhhhhhhhhhhh.eeeee...hhhhhhh..........hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee..hhhhhhhhhhhhhhhhh...eeeee..........eehhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhh............ee.......hhhhhhhhh.....eeeeeee...hhhhhh..............hhhhhhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhh.....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..................eeeee.....eeee..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fpq B   4 EDAELLVTVRGGRLRGIRLKTPGGPVSAFLGIPFAEPPMGPRRFLPPEPKQPWSGVVDATTFQSVCYQYVDTLYPGFEGTEMWNPNRELSEDCLYLNVWTPYPRPTSPTPVLVWIYGGGFYSGASSLDVYDGRFLVQAERTVLVSMNYRVGAFGFLALPGSREAPGNVGLLDQRLALQWVQENVAAFGGDPTSVTLFGEsAGAASVGMHLLSPPSRGLFHRAVLQSGAPNGPWATVGMGEARRRATQLAHLVGCPNDTELVACLRTRPAQVLVNHEWHVLPQESVFRFSFVPVVDGDFLSDTPEALINAGDFHGLQVLVGVVKDEGSYFLVYGAPGFSKDNESLISRAEFLAGVRVGVPQVSDLAAEAVVLHYTDWLHPEDPARLREALSDVVGDHNVVCPVAQLAGRLAAQGARVYAYVFEHRASTLSWPLWMGVPHGYEIEFIFGIPLDPSRNYTAEEKIFAQRLMRYWANFARTGDPNEPRDPQWPPYTAGAQQYVSLDLRPLEVRRGLRAQACAFWNRFLPKLLSA 542
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253    || 269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489    || 502       512       522       532       542
                                                                                                                                                                                                                                 203-SGB                                                258|                                                                                                                                                                                                                                  494|                                            
                                                                                                                                                                                                                                                                                         265                                                                                                                                                                                                                                   498
   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 5FPQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (47, 47)

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
    1PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SGB  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Tyr A:105 - Pro A:106   [ RasMol ]  
    Tyr B:105 - Pro B:106   [ 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
  5fpq
    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
  ACES_HUMAN | P22303
    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)
  3.1.1.7
    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
  ACES_HUMAN | P22303
    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
        ACES_HUMAN | P22303: 1b41 1f8u 1puv 1puw 1vzj 2clj 2x8b 3lii 4bdt 4ey4 4ey5 4ey6 4ey7 4ey8 4m0e 4m0f 4pqe 5foq 5hf5 5hf6 5hf8 5hf9 5hfa

(-) Related Entries Specified in the PDB File

5foq ACETYLCHOLINESTERASE IN COMPLEX WITH C7653
5fpp STRUCTURE OF A PRE-REACTION TERNAY COMPLEX BETWEEN SARIN-ACETYLCHOLINESTERASE AND HI-6