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(-) Description

Title :  SIDEROCALIN-MEDIATED RECOGNITION AND CELLULAR UPTAKE OF ACTINIDES
 
Authors :  B. E. Allred, P. B. Rupert, S. S. Gauny, D. D. An, C. Y. Ralston, M. Sturzbe Hoehne, R. K. Strong, R. J. Abergel
Date :  24 Apr 15  (Deposition) - 05 Aug 15  (Release) - 02 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  Metal Binding Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. E. Allred, P. B. Rupert, S. S. Gauny, D. D. An, C. Y. Ralston, M. Sturzbecher-Hoehne, R. K. Strong, R. J. Abergel
Siderocalin-Mediated Recognition, Sensitization, And Cellular Uptake Of Actinides.
Proc. Natl. Acad. Sci. Usa V. 112 10342 2015
PubMed-ID: 26240330  |  Reference-DOI: 10.1073/PNAS.1508902112

(-) Compounds

Molecule 1 - NEUTROPHIL GELATINASE-ASSOCIATED LIPOCALIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 22-198
    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

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  
Biological Unit 5 (1x):     E 
Biological Unit 6 (1x):      F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 30)

Asymmetric Unit (5, 30)
No.NameCountTypeFull Name
14OL6Ligand/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]
2CL8Ligand/IonCHLORIDE ION
3GOL5Ligand/IonGLYCEROL
4SM6Ligand/IonSAMARIUM (III) ION
5SO45Ligand/IonSULFATE ION
Biological Unit 1 (3, 3)
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]
2CL-1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4SM-1Ligand/IonSAMARIUM (III) ION
5SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
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]
2CL-1Ligand/IonCHLORIDE ION
3GOL-1Ligand/IonGLYCEROL
4SM-1Ligand/IonSAMARIUM (III) ION
5SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 2)
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]
2CL-1Ligand/IonCHLORIDE ION
3GOL-1Ligand/IonGLYCEROL
4SM-1Ligand/IonSAMARIUM (III) ION
5SO41Ligand/IonSULFATE ION
Biological Unit 4 (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]
2CL-1Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL
4SM-1Ligand/IonSAMARIUM (III) ION
5SO4-1Ligand/IonSULFATE ION
Biological Unit 5 (3, 3)
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]
2CL-1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4SM-1Ligand/IonSAMARIUM (III) ION
5SO41Ligand/IonSULFATE ION
Biological Unit 6 (2, 2)
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]
2CL-1Ligand/IonCHLORIDE ION
3GOL-1Ligand/IonGLYCEROL
4SM-1Ligand/IonSAMARIUM (III) ION
5SO41Ligand/IonSULFATE ION

(-) Sites  (30, 30)

Asymmetric Unit (30, 30)
No.NameEvidenceResiduesDescription
01AC1SOFTWARE4OL A:202binding site for residue SM A 201
02AC2SOFTWAREALA A:40 , ILE A:41 , TYR A:52 , SER A:68 , TRP A:79 , ARG A:81 , TYR A:100 , TYR A:106 , PHE A:123 , LYS A:125 , LYS A:134 , SM A:201 , HOH A:307 , HOH A:322 , HOH A:339 , HOH A:344 , HOH A:372binding site for residue 4OL A 202
03AC3SOFTWAREILE A:8 , ASN A:164 , HIS A:165 , HOH A:304 , LYS B:75binding site for residue SO4 A 203
04AC4SOFTWAREGLN A:117 , HIS A:118 , HOH A:302 , ASN E:116binding site for residue GOL A 204
05AC5SOFTWARETHR A:54 , ARG A:81 , TYR A:138 , HOH A:348 , HOH A:388binding site for residue CL A 205
06AC6SOFTWARE4OL B:202binding site for residue SM B 201
07AC7SOFTWAREALA B:40 , ILE B:41 , TYR B:52 , SER B:68 , LEU B:70 , TRP B:79 , TYR B:100 , TYR B:106 , LYS B:125 , LYS B:134 , SM B:201 , HOH B:302 , HOH B:319 , HOH B:323 , HOH B:325 , HOH B:340binding site for residue 4OL B 202
08AC8SOFTWAREASN B:114 , GLN D:117binding site for residue SO4 B 203
09AC9SOFTWARETHR B:54 , TYR B:138 , HOH B:356 , HOH B:374binding site for residue CL B 204
10AD1SOFTWARE4OL C:202binding site for residue SM C 201
11AD2SOFTWAREALA C:40 , ILE C:41 , TYR C:52 , SER C:68 , TRP C:79 , ARG C:81 , TYR C:100 , TYR C:106 , LYS C:125 , LYS C:134 , SM C:201 , HOH C:301 , HOH C:311 , HOH C:314 , HOH C:326 , HOH C:340 , HOH C:342 , HOH D:305binding site for residue 4OL C 202
12AD3SOFTWAREGLN A:117 , ASN C:114 , HOH C:303 , HOH C:306 , HOH C:322binding site for residue SO4 C 203
13AD4SOFTWARETHR C:54 , ARG C:81 , TYR C:138 , HOH C:359binding site for residue CL C 204
14AD5SOFTWARESER C:112 , HIS C:118binding site for residue CL C 205
15AD6SOFTWARE4OL D:202binding site for residue SM D 201
16AD7SOFTWAREALA D:40 , ILE D:41 , TYR D:52 , SER D:68 , TRP D:79 , ARG D:81 , TYR D:106 , LYS D:125 , LYS D:134 , SM D:201 , HOH D:304 , HOH D:307 , HOH D:319 , HOH D:338binding site for residue 4OL D 202
17AD8SOFTWAREASN D:114 , HIS D:118 , ASN F:116binding site for residue GOL D 203
18AD9SOFTWARETHR D:54 , ARG D:81 , TYR D:138 , HOH D:333binding site for residue CL D 204
19AE1SOFTWARELYS D:59 , GLU D:60binding site for residue GOL D 205
20AE2SOFTWARELYS C:75 , ASN D:164 , HIS D:165 , HOH D:315binding site for residue GOL D 206
21AE3SOFTWARESER D:112 , HIS D:118 , ALA D:119binding site for residue CL D 207
22AE4SOFTWARE4OL E:202binding site for residue SM E 201
23AE5SOFTWAREALA E:40 , ILE E:41 , TYR E:52 , SER E:68 , LEU E:70 , TRP E:79 , TYR E:106 , PHE E:123 , LYS E:125 , LYS E:134 , SM E:201 , HOH E:301 , HOH E:310 , HOH E:321 , HOH E:334binding site for residue 4OL E 202
24AE6SOFTWAREARG D:154 , THR E:145 , SER E:146 , HOH E:335binding site for residue SO4 E 203
25AE7SOFTWARETHR E:54 , ARG E:81 , TYR E:138binding site for residue CL E 204
26AE8SOFTWARELYS E:73binding site for residue GOL E 205
27AE9SOFTWARE4OL F:202binding site for residue SM F 201
28AF1SOFTWAREALA F:40 , ILE F:41 , TYR F:52 , SER F:68 , LEU F:70 , TRP F:79 , ARG F:81 , TYR F:106 , LYS F:125 , LYS F:134 , SM F:201 , HOH F:303 , HOH F:313 , HOH F:314 , HOH F:316 , HOH F:349 , HOH F:356binding site for residue 4OL F 202
29AF2SOFTWARELYS E:75 , PRO F:162 , ASN F:164 , HIS F:165binding site for residue SO4 F 203
30AF3SOFTWARETHR F:54 , ARG F:81 , TYR F:138binding site for residue CL F 204

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:76 -A:175
2B:76 -B:175
3C:76 -C:175
4D:76 -D:175
5E:76 -E:175
6F:76 -F:175

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZHH)

(-) 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:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 4zhh A   2 DSTSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCIDG 178
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       


Chain B from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 4zhh 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
                 4zhh C   3 STSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 177
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172     


Chain D from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 4zhh D   2 DSTSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 177
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171      


Chain E from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                
               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
                 4zhh E   2 DSTSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 177
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171      


Chain F 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
                 4zhh F   3 STSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGSQPGEFTLGNIKSYPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCID 177
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172
   Legend:   → Mismatch (orange background)
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  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 4ZHH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

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  4zhh
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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 5jr8 5khp 5kic 5kid

(-) Related Entries Specified in the PDB File

4zhc 4zhd 4zhf 4zhg