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 HOLO FORM OF A PERIPLASMIC HEME BINDING PROTEIN
 
Authors :  D. Mattle, B. A. Goetz, J. S. Woo, K. P. Locher
Date :  06 Jul 10  (Deposition) - 13 Oct 10  (Release) - 09 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transport Protein, Alpha Beta Protein, Rigid Helical Backbone, Substrate-Bound, Iron Transport, Heme Transport, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Mattle, A. Zeltina, J. S. Woo, B. A. Goetz, K. P. Locher
Two Stacked Heme Molecules In The Binding Pocket Of The Periplasmic Heme-Binding Protein Hmut From Yersinia Pestis.
J. Mol. Biol. V. 404 220 2010
PubMed-ID: 20888343  |  Reference-DOI: 10.1016/J.JMB.2010.09.005

(-) Compounds

Molecule 1 - HEMIN-BINDING PERIPLASMIC PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: HMUT, Y0541, YPA_4001, YPO0281, YP_0436
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 360102
    Strain: ANTIQUA

 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  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:100 , SER A:104 , MET A:165 , HIS A:167 , LEU A:170 , TYR A:200 , HEM A:302BINDING SITE FOR RESIDUE HEM A 301
2AC2SOFTWARETYR A:70 , ARG A:72 , GLN A:101 , THR A:179 , ALA A:180 , ALA A:181 , TYR A:200 , MET A:255 , LEU A:258 , HEM A:301 , HOH A:306 , HOH A:339BINDING SITE FOR RESIDUE HEM A 302
3AC3SOFTWARESER B:104 , MET B:165 , HIS B:167 , LEU B:170 , MET B:173 , TYR B:200 , LEU B:258 , HEM B:302BINDING SITE FOR RESIDUE HEM B 301
4AC4SOFTWARETHR B:55 , TYR B:70 , ARG B:72 , LEU B:97 , GLN B:101 , THR B:179 , ALA B:180 , ALA B:181 , ARG B:199 , TYR B:200 , MET B:255 , HEM B:301BINDING SITE FOR RESIDUE HEM B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NU1)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gln A:58 -Pro A:59
2Gln A:94 -Pro A:95
3Gln B:58 -Pro B:59
4Gln B:94 -Pro B:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NU1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NU1)

(-) Exons   (0, 0)

(no "Exon" information available for 3NU1)

(-) 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:254
 aligned with A0A0E1NWS3_Y | A0A0E1NWS3 from UniProtKB/TrEMBL  Length:279

    Alignment length:254
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275    
         A0A0E1NWS3_Y    26 AERIVTIGGDVTEIAYALGAGDEIVARDSTSQQPQAAQKLPDVGYMRTLNAEGILAMKPTMLLVSELAQPSLVLTQIASSGVNVVTVPGQTTPESVAMKINAVATALHQTEKGQKLIEDYQQRLAAVNKTPLPVKVLFVMSHGGLTPMAAGQNTAADAMIRAAGGSNAMQGFSRYRPLSQEGVIASAPDLLLITTDGVKALGSSENIWKLPGMALTPAGKHKRLLVVDDMALLGFGLETPQVLAQLREKMEQMQ 279
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeehhhhhhhhhhhhhhh.eeee......hhhhhh..........hhhhhhh....eeeee....hhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeee.......eee...hhhhhhhhhh..ee.......eee.hhhhhhhhh..eeeeehhhhhhhhhhhhhhh..hhhhhhhhhh..eeeehhhhhhh...hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nu1 A  26 AERIVTIGGDVTEIAYALGAGDEIVARDSTSQQPQAAQKLPDVGYMRTLNAEGILAMKPTMLLVSELAQPSLVLTQIASSGVNVVTVPGQTTPESVAMKINAVATALHQTEKGQKLIEDYQQRLAAVNKTPLPVKVLFVMSHGGLTPMAAGQNTAADAMIRAAGGSNAMQGFSRYRPLSQEGVIASAPDLLLITTDGVKALGSSENIWKLPGMALTPAGKHKRLLVVDDMALLGFGLETPQVLAQLREKMEQMQ 279
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275    


Chain B from PDB  Type:PROTEIN  Length:254
 aligned with A0A0E1NWS3_Y | A0A0E1NWS3 from UniProtKB/TrEMBL  Length:279

    Alignment length:254
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275    
         A0A0E1NWS3_Y    26 AERIVTIGGDVTEIAYALGAGDEIVARDSTSQQPQAAQKLPDVGYMRTLNAEGILAMKPTMLLVSELAQPSLVLTQIASSGVNVVTVPGQTTPESVAMKINAVATALHQTEKGQKLIEDYQQRLAAVNKTPLPVKVLFVMSHGGLTPMAAGQNTAADAMIRAAGGSNAMQGFSRYRPLSQEGVIASAPDLLLITTDGVKALGSSENIWKLPGMALTPAGKHKRLLVVDDMALLGFGLETPQVLAQLREKMEQMQ 279
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeehhhhhhhhhhh.hhh.eeee.......hhhhhh.........hhhhhhh....eeeee....hhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee.......eee...hhhhhhhhhh..ee.......eee.hhhhhhhh...eeeeehhhhhhhhhhhhhh.......hhhhhhh.eeeehhhhhhh...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nu1 B  26 AERIVTIGGDVTEIAYALGAGDEIVARDSTSQQPQAAQKLPDVGYMRTLNAEGILAMKPTMLLVSELAQPSLVLTQIASSGVNVVTVPGQTTPESVAMKINAVATALHQTEKGQKLIEDYQQRLAAVNKTPLPVKVLFVMSHGGLTPMAAGQNTAADAMIRAAGGSNAMQGFSRYRPLSQEGVIASAPDLLLITTDGVKALGSSENIWKLPGMALTPAGKHKRLLVVDDMALLGFGLETPQVLAQLREKMEQMQ 279
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275
   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 3NU1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NU1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3NU1)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3NU1)

 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
    HEM  [ 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
    Gln A:58 - Pro A:59   [ RasMol ]  
    Gln A:94 - Pro A:95   [ RasMol ]  
    Gln B:58 - Pro B:59   [ RasMol ]  
    Gln B:94 - Pro B:95   [ 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
  3nu1
    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
  A0A0E1NWS3_Y | A0A0E1NWS3
    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
  A0A0E1NWS3_Y | A0A0E1NWS3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3NU1)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3NU1)