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(-) Description

Title :  ENGINEERED HUMAN LIPOCALIN 2 (LCN2), APO-FORM
 
Authors :  D. L. Schonfeld, L. Chatwell, A. Skerra
Date :  11 Jan 08  (Deposition) - 20 Jan 09  (Release) - 20 Jan 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
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)
Biol. Unit 7:  G  (1x)
Biol. Unit 8:  H  (1x)
Keywords :  Protein Design, Ligand Binding Protein, De Novo Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. L. Schonfeld, G. Matschiner, L. Chatwell, S. Trentmann, S. Schlehuber, A. Hohlbaum, A. Skerra
High Affinity Molecular Recognition And Functional Blockade Of Ctla-4 By An Engineered Human Lipocalin
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENGINEERED HUMAN LIPOCALIN 2
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNGAL62
    Expression System Strain: W3110
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Synonym: ENGINEERED LCN2, ENGINEERED NEUTROPHIL-GELATINASE ASSOCIATED LIPOCALIN, ENGINEERED SIDEROCALIN

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
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  
Biological Unit 7 (1x):       G 
Biological Unit 8 (1x):        H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
11PE3Ligand/IonPENTAETHYLENE GLYCOL
2PE55Ligand/Ion3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2PE5-1Ligand/Ion3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
2PE51Ligand/Ion3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
2PE51Ligand/Ion3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
2PE51Ligand/Ion3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2PE5-1Ligand/Ion3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
2PE51Ligand/Ion3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
Biological Unit 7 (1, 1)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2PE5-1Ligand/Ion3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
Biological Unit 8 (1, 1)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
2PE51Ligand/Ion3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:52 , ILE B:70 , ALA B:81 , LEU B:94 , PHE B:123BINDING SITE FOR RESIDUE PE5 B 179
2AC2SOFTWARETYR C:52 , SER C:68 , ILE C:70 , THR C:79 , PHE C:83 , PHE C:123 , HOH C:237BINDING SITE FOR RESIDUE PE5 C 179
3AC3SOFTWAREPHE D:123 , PHE D:132 , THR D:136 , TYR D:138BINDING SITE FOR RESIDUE PE5 D 179
4AC4SOFTWARETYR F:52 , ILE F:70 , TYR F:106 , PHE F:123 , LEU F:125 , PHE F:132BINDING SITE FOR RESIDUE PE5 F 179
5AC5SOFTWARETYR H:52 , ALA H:81 , PHE H:123 , PHE H:132 , HOH H:321 , HOH H:322BINDING SITE FOR RESIDUE PE5 H 179
6AC6SOFTWAREILE A:41 , SER A:68 , THR A:79 , TYR A:106 , PHE A:123 , HOH A:236 , HOH A:244BINDING SITE FOR RESIDUE 1PE A 179
7AC7SOFTWARESER E:68 , PHE E:83 , TYR E:106 , PHE E:123 , PHE E:132BINDING SITE FOR RESIDUE 1PE E 179

(-) SS Bonds  (8, 8)

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
7G:76 -G:175
8H:76 -H:175

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BX8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BX8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BX8)

(-) Exons   (0, 0)

(no "Exon" information available for 3BX8)

(-) 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:167
                                                                                                                                                                                                       
               SCOP domains d3bx8a_ A: automated matches                                                                                                                                            SCOP domains
               CATH domains 3bx8A00 A:5-178  [code=2.40.128.20, no name defined]                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh......hhhhhheeeeeeeeee..............eeeeee.....eeeeeeeee..eeeeeeeeeee.....eeee......eeeeeeee....eeeeeeee....eeeeeeee.....hhhhhhhhhhhhhhh..hhh.ee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bx8 A   5 SDLIPAPPLSKVPLQQNFQDNQFHGKWYVVGLAGNRILRDDQHPMNMYATIYELKEDKSYNVTSVISSHKKCEYTIATFVPGSQPGEFTLGIKSYSYLVRVVSTDYNQYAVVFFKLAEAEFFAITIYGRTKELASELKENFIRFSKSLGLPENHIVFPVPIDQCIDG 178
                                    14        24        34        44        54        64        74        84        94||  || 109       119       131       141       151       161       171       
                                                                                                                     95|  ||                   127|                                                
                                                                                                                      97  ||                    130                                                
                                                                                                                        100|                                                                       
                                                                                                                         105                                                                       


Chain B from PDB  Type:PROTEIN  Length:166
                                                                                                                                                                                                      
               SCOP domains d3bx8b_ B: automated matches                                                                                                                                           SCOP domains
               CATH domains 3bx8B00 B:4-177  [code=2.40.128.20, no name defined]                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh......hhhhhheeeeeeeeee..............eeeeee.....eeeeeeeee..eeeeeeeeeee.....eeee....eeeeeeee....eeeeeeee.....eeeeeeee.....hhhhhhhhhhhhhhh..hhh.ee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bx8 B   4 TSDLIPAPPLSKVPLQQNFQDNQFHGKWYVVGLAGNRILRDDQHPMNMYATIYELKEDKSYNVTSVISSHKKCEYTIATFVPGSQPGEFTLGNTSYLVRVVSTDYNQYAVVFFKLADNAEFFAITIYGRTKELASELKENFIRFSKSLGLPENHIVFPVPIDQCID 177
                                    13        23        33        43        53        63        73        83        93  ||   110       120     ||131       141       151       161       171      
                                                                                                                       96|                   126|                                                 
                                                                                                                       104                    128                                                 


Chain C from PDB  Type:PROTEIN  Length:167
                                                                                                                                                                                                       
               SCOP domains d3bx8c_ C: automated matches                                                                                                                                            SCOP domains
               CATH domains 3bx8C00 C:5-178  [code=2.40.128.20, no name defined]                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh......hhhhhheeeeeeeeee..............eeeeee.....eeeeeeeee..eeeeeeeeeee.....eeee......eeeeeeee....eeeeeeee....eeeeeeee.....hhhhhhhhhhhhhhh..hhh.ee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bx8 C   5 SDLIPAPPLSKVPLQQNFQDNQFHGKWYVVGLAGNRILRDDQHPMNMYATIYELKEDKSYNVTSVISSHKKCEYTIATFVPGSQPGEFTLGIKSYSYLVRVVSTDYNQYAVVFFKLAEAEFFAITIYGRTKELASELKENFIRFSKSLGLPENHIVFPVPIDQCIDG 178
                                    14        24        34        44        54        64        74        84        94||  || 109       119       131       141       151       161       171       
                                                                                                                     95|  ||                   127|                                                
                                                                                                                      97  ||                    130                                                
                                                                                                                        100|                                                                       
                                                                                                                         105                                                                       


Chain D from PDB  Type:PROTEIN  Length:168
                                                                                                                                                                                                        
               SCOP domains d3bx8d_ D: automated matches                                                                                                                                             SCOP domains
               CATH domains 3bx8D00 D:4-177  [code=2.40.128.20, no name defined]                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhh......hhhhhheeeeeeeeee..............eeeeee.....eeeeeeeee..eeeeeeeeeee.....eeee....eeeeeeeee....eeeeeeeee.....eeeeeeee.....hhhhhhhhhhhhhhh..hhh.ee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3bx8 D   4 TSDLIPAPPLSKVPLQQNFQDNQFHGKWYVVGLAGNRILRDDQHPMNMYATIYELKEDKSYNVTSVISSHKKCEYTIATFVPGSQPGEFTLGNITSYLVRVVSTDYNQYAVVFFKLAEDNAEFFAITIYGRTKELASELKENFIRFSKSLGLPENHIVFPVPIDQCID 177
                                    13        23        33        43        53        63        73        83        93   ||  109       119       129       139       149       159       169        
                                                                                                                        97|                                                                         
                                                                                                                        104                                                                         


Chain E from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                  
               SCOP domains d3bx8e_ E: automated matches                                                                                                                                       SCOP domains
               CATH domains 3bx8E00 E:5-178  [code=2.40.128.20, no name defined]                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhh............eeeeeeeeee..............eeeeee.....eeeeeeeee..eeeeeeeeeee.....eee...eeeeeeee....eeeeeeee...eeeeeeee.....hhhhhhhhhhhhhhh..hhh.ee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3bx8 E   5 SDLIPAPPLSKVPLQQNFQDNQFHGKWYVVGLAGNRILRDDQHPMNMYATIYELKEDKSYNVTSVISSHKKCEYTIATFVPGSQPGEFTLTSYLVRVVSTDYNQYAVVFFKLAEEFFAITIYGRTKELASELKENFIRFSKSLGLPENHIVFPVPIDQCIDG 178
                                    14        24        34        44        54        64        74        84        94|      113       123   ||  136       146       156       166       176  
                                                                                                                    94|                    127|                                               
                                                                                                                    104                     131                                               


Chain F from PDB  Type:PROTEIN  Length:158
                                                                                                                                                                                              
               SCOP domains d3bx8f_ F: automated matches                                                                                                                                   SCOP domains
               CATH domains 3bx8F00 F:4-177  [code=2.40.128.20, no name defined]                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh.....hhhhhheeeeeeeeee..............eeeeee.....eeeeeee....eeeeeeeee.....eeee..eeeeeee.....eeeeeeee..eeeeeeee.....hhhhhhhhhhhhhh...hhh.ee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bx8 F   4 TSDLIPAPPLSKVPLQQFQDNQFHGKWYVVGLAGNRILRDDQHPMNMYATIYELKEDKSYNVTSVISSKCEYTIATFVPGSQPGEFTLGSYLVRVVSTDYNQYAVVFFKLAEFFAITIYGRTKELASELKENFIRFSKSLGLPENHIVFPVPIDQCID 177
                                    13      ||24        34        44        54        64       |76        86       105       115       125||     139       149       159       169        
                                           20|                                                72|                  95|                  126|                                              
                                            22                                                 75                  105                   131                                              


Chain G from PDB  Type:PROTEIN  Length:161
                                                                                                                                                                                                 
               SCOP domains d3bx8g_ G: automated matches                                                                                                                                      SCOP domains
               CATH domains 3bx8G00 G:4-178  [code=2.40.128.20, no name defined]                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh.....hhhhhheeeeeeeeee..............eeeeee.....eeeeeeee...eeeeeeeeee.....eeee..eeeeeeee....eeeeeeee...eeeeeeee.....hhhhhhhhhhhhhh...hhh.ee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bx8 G   4 TSDLIPAPPLSKVPLQQFQDNQFHGKWYVVGLAGNRILRDDQHPMNMYATIYELKEDKSYNVTSVISSHKCEYTIATFVPGSQPGEFTLGSYLVRVVSTDYNQYAVVFFKLAEEFFAITIYGRTKELASELKENFIRFSKSLGLPENHIVFPVPIDQCIDG 178
                                    13      ||24        34        44        54        64        75        85        95|      114       124  ||   137       147       157       167       177 
                                           20|                                                 73|                  95|                   127|                                               
                                            22                                                  75                  105                    131                                               


Chain H from PDB  Type:PROTEIN  Length:161
                                                                                                                                                                                                 
               SCOP domains d3bx8h_ H: automated matches                                                                                                                                      SCOP domains
               CATH domains 3bx8H00 H:5-177  [code=2.40.128.20, no name defined]                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh...........eeeeeeeeee..............eeeeee.....eeeeeeeee..eeeeeeeeeee.....eee...eeeeeeeee....eeeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhh..hhh.ee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bx8 H   5 SDLIPAPPLSKVPLQQFQDNQFHGKWYVVGLAGNRILRDDQHPMNMYATIYELKEDKSYNVTSVISSHKKCEYTIATFVPGSQPGEFTLGTSYLVRVVSTDYNQYAVVFFKLAEEFFAITIYGRTKELASELKENFIRFSKSLGLPENHIVFPVPIDQCID 177
                                    14     || 25        35        45        55        65        75        85        95|      113       123   ||  136       146       156       166       176 
                                          20|                                                                       95|                    127|                                              
                                           22                                                                       104                     131
   Legend:   → Mismatch (orange background)
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  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, 8)

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

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BX8)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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 Related Entries

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(-) Related Entries Specified in the PDB File

3bx7 ENGINEERED HUMAN LCN2 IN COMPLEX WITH HUMAN CTLA4