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(-) Description

Title :  DISPOSAL OF IRON BY A MUTANT FORM OF SIDEROCALIN NGAL
 
Authors :  P. B. Rupert, R. K. Strong, J. Barasch, M. Hollman, R. Deng, E. A. Hod, R. A B. Allred, K. Xu, S. Darrah, Y. Tekabe, A. Perlstein, E. Bruck, J. Staub K. Corbin, C. Buchen, V. Slavkovich, J. Graziano, S. Spitalnik, A. Qiu
Date :  05 May 16  (Deposition) - 28 Sep 16  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A  (1x)
Biol. Unit 4:  B  (2x)
Keywords :  Fe-Siderophore Binding Protein Mutant, Siderophore Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Barasch, M. Hollmen, R. Deng, E. A. Hod, P. B. Rupert, R. J. Abergel, B. E. Allred, K. Xu, S. F. Darrah, Y. Tekabe, A. Perlstein, R. Wax, E. Bruck, J. Stauber, K. A. Corbin, C. Buchen, V. Slavkovich, J. Graziano, S. L. Spitalnik, G. Bao, R. K. Strong, A. Qiu
Disposal Of Iron By A Mutant Form Of Lipocalin 2.
Nat Commun V. 7 12973 2016
PubMed-ID: 27796299  |  Reference-DOI: 10.1038/NCOMMS12973

(-) Compounds

Molecule 1 - NEUTROPHIL GELATINASE-ASSOCIATED LIPOCALIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Gene: LCN2, HNL, NGAL
    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

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): A 
Biological Unit 4 (2x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PO43Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 4 (2, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PO44Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:81 , TYR A:106 , LYS A:125 , LYS A:134 , HOH A:302 , HOH A:314 , HOH A:322binding site for residue PO4 A 201
2AC2SOFTWARETYR B:52 , THR B:54 , SER B:68 , ARG B:81 , LYS B:134 , TYR B:138 , PO4 B:203binding site for residue PO4 B 201
3AC3SOFTWAREILE A:55 , GLU A:57 , TYR A:78 , LEU B:18 , GLN B:19 , GLN B:20 , VAL B:111 , SER B:112binding site for residue GOL B 202
4AC4SOFTWARETRP B:79 , ARG B:81 , TYR B:106 , LYS B:125 , LYS B:134 , PO4 B:201 , HOH B:305binding site for residue PO4 B 203

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:76 -A:175
2A:87 -B:87
3B:76 -B:175

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5JR8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JR8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JR8)

(-) Exons   (0, 0)

(no "Exon" information available for 5JR8)

(-) 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:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh......hhhhhheeeeeeeeee..............eeeeee.....eeeeeeee...eeeeeeeeee.....eeee.hhhhh..eeeeeeeeeee....eeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhh..hhh.ee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jr8 A   6 DLIPAPPLSSVPLQQNFQDNQFQGKWYVVGLAGNAILREDEDPQKMYATIYELKEDKSYNVTSVLFRDGCDYWIRTFVPGCQPGEFTLGNIQSYPGLTSYLVRVVSTNYNQFAMVFFKKVSQNQEYFKITLYGRTKELTSELQENFIRFSKSLGLPENNIVFPVPIDQCIDG 178
                                    15        25        35        45        55        65      ||76        86        96       106       116       126       136       146       156       166       176  
                                                                                             72|                                                                                                        
                                                                                              74                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:173
                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 5jr8 B   5 SDLIPAPPLSSVPLQQNFQDNQFQGKWYVVGLAGNAILREDEDPQKMYATIYELKEDKSYNVTSVLFRDDGCDYWIRTFVPGCQPGEFTLGNIQSYPGLTSYLVRVVSTNYNQFAMVFFKKVSQNQEYFKITLYGRTKELTSELQENFIRFSKSLGLPENNIVFPVPIDQCID 177
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174
   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 5JR8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JR8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JR8)

(-) Gene Ontology  (15, 15)

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  5jr8
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  NGAL_HUMAN | P80188
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 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 4k19 4mvi 4mvk 4mvl 4qae 4zfx 4zhc 4zhd 4zhf 4zhg 4zhh 5khp 5kic 5kid

(-) Related Entries Specified in the PDB File

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