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
(-)Biological Unit 3
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  THE STRUCTURE OF HUMAN SIDEROCALIN BOUND TO THE BACTERIAL SIDEROPHORE FLUVIBACTIN
 
Authors :  C. Correnti, M. C. Clifton, R. K. Strong
Date :  04 Apr 13  (Deposition) - 31 Jul 13  (Release) - 23 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.74
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Beta Barrel, Antibacterial, Siderophore, Metal Binding Protein- Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. E. Allred, C. Correnti, M. C. Clifton, R. K. Strong, K. N. Raymond
Siderocalin Outwits The Coordination Chemistry Of Vibriobactin, A Siderophore Of Vibrio Cholerae.
Acs Chem. Biol. V. 8 1882 2013
PubMed-ID: 23755875  |  Reference-DOI: 10.1021/CB4002552

(-) Compounds

Molecule 1 - NEUTROPHIL GELATINASE-ASSOCIATED LIPOCALIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 21-198
    Gene: LCN2, HNL, NGAL
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NGAL, 25 KDA ALPHA-2-MICROGLOBULIN-RELATED SUBUNIT OF MMP-9, LIPOCALIN-2, ONCOGENE 24P3, SIDEROCALIN LCN2, P25

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 15)

Asymmetric Unit (6, 15)
No.NameCountTypeFull Name
11OD3Ligand/Ion(4S,5R)-N,N-BIS{3-[(2,3-DIHYDROXYBENZOYL)AMINO]PROPYL}-2-(2,3-DIHYDROXYPHENYL)-5-METHYL-4,5-DIHYDRO-1,3-OXAZOLE-4-CARBOXAMIDE
2CL2Ligand/IonCHLORIDE ION
3FE3Ligand/IonFE (III) ION
4GOL3Ligand/IonGLYCEROL
5NA2Ligand/IonSODIUM ION
6SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
11OD1Ligand/Ion(4S,5R)-N,N-BIS{3-[(2,3-DIHYDROXYBENZOYL)AMINO]PROPYL}-2-(2,3-DIHYDROXYPHENYL)-5-METHYL-4,5-DIHYDRO-1,3-OXAZOLE-4-CARBOXAMIDE
2CL-1Ligand/IonCHLORIDE ION
3FE-1Ligand/IonFE (III) ION
4GOL2Ligand/IonGLYCEROL
5NA-1Ligand/IonSODIUM ION
6SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
11OD1Ligand/Ion(4S,5R)-N,N-BIS{3-[(2,3-DIHYDROXYBENZOYL)AMINO]PROPYL}-2-(2,3-DIHYDROXYPHENYL)-5-METHYL-4,5-DIHYDRO-1,3-OXAZOLE-4-CARBOXAMIDE
2CL-1Ligand/IonCHLORIDE ION
3FE-1Ligand/IonFE (III) ION
4GOL-1Ligand/IonGLYCEROL
5NA-1Ligand/IonSODIUM ION
6SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (3, 3)
No.NameCountTypeFull Name
11OD1Ligand/Ion(4S,5R)-N,N-BIS{3-[(2,3-DIHYDROXYBENZOYL)AMINO]PROPYL}-2-(2,3-DIHYDROXYPHENYL)-5-METHYL-4,5-DIHYDRO-1,3-OXAZOLE-4-CARBOXAMIDE
2CL-1Ligand/IonCHLORIDE ION
3FE-1Ligand/IonFE (III) ION
4GOL1Ligand/IonGLYCEROL
5NA-1Ligand/IonSODIUM ION
6SO41Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARE1OD A:206BINDING SITE FOR RESIDUE FE A 201
02AC2SOFTWAREASN A:114 , HIS A:118BINDING SITE FOR RESIDUE GOL A 202
03AC3SOFTWARELEU A:36 , TYR A:52 , LYS A:134 , 1OD A:206 , HOH A:318BINDING SITE FOR RESIDUE SO4 A 203
04AC4SOFTWAREARG A:130BINDING SITE FOR RESIDUE CL A 204
05AC5SOFTWARELEU A:42 , ASN A:164 , HIS A:165 , LYS C:75BINDING SITE FOR RESIDUE GOL A 205
06AC6SOFTWARESER A:68 , TRP A:79 , ARG A:81 , LEU A:94 , TYR A:100 , LEU A:103 , TYR A:106 , LYS A:125 , TYR A:132 , LYS A:134 , FE A:201 , SO4 A:203BINDING SITE FOR RESIDUE 1OD A 206
07AC7SOFTWARE1OD B:202BINDING SITE FOR RESIDUE FE B 201
08AC8SOFTWAREALA B:40 , TRP B:79 , LEU B:94 , LEU B:103 , TYR B:106 , PHE B:123 , LYS B:125 , LYS B:134 , FE B:201BINDING SITE FOR RESIDUE 1OD B 202
09AC9SOFTWARE1OD C:207BINDING SITE FOR RESIDUE FE C 201
10BC1SOFTWARELEU C:36 , ILE C:41 , TYR C:52 , LYS C:134 , 1OD C:207 , HOH C:334BINDING SITE FOR RESIDUE SO4 C 202
11BC2SOFTWAREGLN A:117 , ASN C:114 , HIS C:118BINDING SITE FOR RESIDUE GOL C 206
12BC3SOFTWARETYR C:52 , SER C:68 , TRP C:79 , ARG C:81 , LEU C:94 , TYR C:100 , LEU C:103 , TYR C:106 , LYS C:125 , LYS C:134 , FE C:201 , SO4 C:202BINDING SITE FOR RESIDUE 1OD C 207

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:76 -A:175
2B:76 -B:175
3C:76 -C:175

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4K19)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K19)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K19)

(-) Exons   (0, 0)

(no "Exon" information available for 4K19)

(-) 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:174
                                                                                                                                                                                                              
               SCOP domains d4k19a_ A: Neutrophil gelatinase-associated lipocalin (NGAL)                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhh............eeeeeeeeee..............eeeeee.....eeeeeeeee..eeeeeeeeeee.....eeee.hhhhh..eeeeeeeeeee....eeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhh..hhh.ee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4k19 A   5 SDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCIDG 178
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174    


Chain B from PDB  Type:PROTEIN  Length:163
                                                                                                                                                                                                   
               SCOP domains d4k19b_ B: Neutrophil gelatinase-associated lipocalin (NGAL)                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh......hhhhhheeeeeeeee.............eeeee....eeeeeeeee..eeeeeeeeeee.....eeee.hhhhh..eeeeeeeeee...eeeeeeeeee..eeeeeeeeee.......hhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k19 B   5 SDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLANAILREDKPQKMYATIYELDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNQHAMVFFKKVSQNREYFKITLYGRTKELTKENFIRFSKSLGLPENHIVFPVPIDQCI 176
                                    14        24        34  ||    45||      56 ||     68        78        88        98       108    || 120       130       140    || 153       163       173   
                                                           37|     46|        58|                                                 113|                          145|                           
                                                            39      48         61                                                  116                           149                           


Chain C from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                
               SCOP domains d4k19c_ C: Neutrophil gelatinase-associated lipocalin (NGAL)                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh......hhhhhheeeeeeeeee..............eeeeee.....eeeeeeeee..eeeeeeeeeee.....eeee.hhhhh..eeeeeeeeeee....eeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhh..hhh.ee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k19 C   2 DSTSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 177
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
   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  (1, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K19)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K19)

(-) Gene Ontology  (15, 15)

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
    1OD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4k19)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 3 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
  4k19
    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
  NGAL_HUMAN | P80188
    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
  NGAL_HUMAN | P80188
    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
        NGAL_HUMAN | P80188: 1dfv 1l6m 1ngl 1qqs 1x71 1x89 1x8u 3by0 3cbc 3cmp 3dsz 3dtq 3fw4 3fw5 3hwd 3hwe 3hwf 3hwg 3i0a 3k3l 3pec 3ped 3t1d 3tf6 3tzs 3u03 3u0d 4gh7 4iaw 4iax 4mvi 4mvk 4mvl 4qae 4zfx 4zhc 4zhd 4zhf 4zhg 4zhh 5jr8 5khp 5kic 5kid

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4K19)