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(-) Description

Title :  LONG-SOUGHT STABILIZATION OF BERKELIUM(IV) IN SOLUTION: AN ANOMALY WITHIN THE HEAVY ACTINIDE SERIES
 
Authors :  P. B. Rupert, R. K. Strong
Date :  16 Jun 16  (Deposition) - 26 Apr 17  (Release) - 10 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Siderophore-Binding, Ngal, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. J. -P. Deblonde, M. Sturzbecher-Hoehne, P. B. Rupert, D. D. An, M. -C. Illy, C. Y. Ralston, J. Brabec, W. A. De Jong, R. K. Strong, R. J. Abergel
Chelation And Stabilization Of Berkelium In Oxidation State +Iv
Nat. Chem. 2017
PubMed: search  |  Reference-DOI: 10.1038/NCHEM.2759

(-) Compounds

Molecule 1 - NEUTROPHIL GELATINASE-ASSOCIATED LIPOCALIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    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

  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  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
14OL3Ligand/IonN,N'-BUTANE-1,4-DIYLBIS[1-HYDROXY-N-(3-{[(1-HYDROXY-6-OXO-1,6-DIHYDROPYRIDIN-2-YL)CARBONYL]AMINO}PROPYL)-6-OXO-1,6-DIHYDROPYRIDINE-2-CARBOXAMIDE]
2CF3Ligand/IonCALIFORNIUM ION
3CL3Ligand/IonCHLORIDE ION
4SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
14OL1Ligand/IonN,N'-BUTANE-1,4-DIYLBIS[1-HYDROXY-N-(3-{[(1-HYDROXY-6-OXO-1,6-DIHYDROPYRIDIN-2-YL)CARBONYL]AMINO}PROPYL)-6-OXO-1,6-DIHYDROPYRIDINE-2-CARBOXAMIDE]
2CF-1Ligand/IonCALIFORNIUM ION
3CL-1Ligand/IonCHLORIDE ION
4SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
14OL1Ligand/IonN,N'-BUTANE-1,4-DIYLBIS[1-HYDROXY-N-(3-{[(1-HYDROXY-6-OXO-1,6-DIHYDROPYRIDIN-2-YL)CARBONYL]AMINO}PROPYL)-6-OXO-1,6-DIHYDROPYRIDINE-2-CARBOXAMIDE]
2CF-1Ligand/IonCALIFORNIUM ION
3CL-1Ligand/IonCHLORIDE ION
4SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
14OL1Ligand/IonN,N'-BUTANE-1,4-DIYLBIS[1-HYDROXY-N-(3-{[(1-HYDROXY-6-OXO-1,6-DIHYDROPYRIDIN-2-YL)CARBONYL]AMINO}PROPYL)-6-OXO-1,6-DIHYDROPYRIDINE-2-CARBOXAMIDE]
2CF-1Ligand/IonCALIFORNIUM ION
3CL-1Ligand/IonCHLORIDE ION
4SO43Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARE4OL A:202binding site for residue CF A 201
02AC2SOFTWAREALA A:40 , ILE A:41 , TYR A:52 , SER A:68 , TRP A:79 , ARG A:81 , TYR A:106 , PHE A:123 , LYS A:125 , TYR A:132 , LYS A:134 , CF A:201 , HOH A:303binding site for residue 4OL A 202
03AC3SOFTWARETHR A:54 , TYR A:138binding site for residue CL A 203
04AC4SOFTWARE4OL B:202binding site for residue CF B 201
05AC5SOFTWAREALA B:40 , ILE B:41 , TYR B:52 , SER B:68 , TRP B:79 , ARG B:81 , TYR B:100 , TYR B:106 , PHE B:123 , LYS B:125 , TYR B:132 , PHE B:133 , LYS B:134 , CF B:201 , HOH B:302binding site for residue 4OL B 202
06AC6SOFTWARETHR B:54 , TYR B:138binding site for residue CL B 203
07AC7SOFTWARE4OL C:202binding site for residue CF C 201
08AC8SOFTWAREALA C:40 , ILE C:41 , TYR C:52 , SER C:68 , TRP C:79 , ARG C:81 , TYR C:100 , TYR C:106 , PHE C:123 , LYS C:125 , TYR C:132 , LYS C:134 , CF C:201 , CL C:203 , HOH C:303binding site for residue 4OL C 202
09AC9SOFTWARETHR C:54 , TYR C:138 , 4OL C:202binding site for residue CL C 203
10AD1SOFTWAREPRO A:162 , ASN A:164 , HIS A:165 , LYS C:75binding site for residue SO4 C 204
11AD2SOFTWAREGLN A:117 , ASN C:114 , HIS C:118binding site for residue SO4 C 205
12AD3SOFTWARELYS A:75 , ASN C:164 , HIS C:165binding site for residue SO4 C 206

(-) 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 5KIC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KIC)

(-) 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: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
                 5kic A   5 SDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 177
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174   


Chain B from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               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
                 5kic B   3 STSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 177
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172     


Chain C from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               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
                 5kic C   3 STSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 177
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172
   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 5KIC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)

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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 5jr8 5khp 5kid

(-) Related Entries Specified in the PDB File

5khp 5kid