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(-) Description

Title :  CRYSTAL STRUCTURE OF JUVENILE HORMONE BINDING PROTEIN FROM SILKWORM
 
Authors :  R. Suzuki, Z. Fujimoto, T. Shiotsuki, M. Momma, A. Tase, T. Yamazaki
Date :  27 Apr 09  (Deposition) - 28 Apr 10  (Release) - 15 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Juvenile Hormone, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Fujimoto, R. Suzuki, T. Shiotsuki, W. Tsuchiya, A. Tase, M. Momma, T. Yamazaki
Crystal Structure Of Silkworm Bombyx Mori Jhbp In Complex With 2-Methyl-2, 4-Pentanediol: Plasticity Of Jh-Binding Pocket And Ligand-Induced Conformational Change Of The Second Cavity In Jhbp
Plos One V. 8 56261 2013
PubMed-ID: 23437107  |  Reference-DOI: 10.1371/JOURNAL.PONE.0056261
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMOLYMPH JUVENILE HORMONE BINDING PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-2T
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 19-243
    Gene: HJHBP
    Organism Common: SILK MOTH
    Organism Scientific: BOMBYX MORI
    Organism Taxid: 7091

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 28)

Asymmetric Unit (2, 28)
No.NameCountTypeFull Name
1MPD8Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2ZN20Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2ZN-1Ligand/IonZINC ION

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:36 , TRP A:38 , HIS A:206 , HOH A:258 , GLU C:107BINDING SITE FOR RESIDUE ZN A 226
02AC2SOFTWAREASP A:135 , HIS A:141 , HOH A:251 , GLU C:170BINDING SITE FOR RESIDUE ZN A 227
03AC3SOFTWAREHIS A:96 , ASP A:119 , HOH A:253 , HOH A:254 , GLU C:26BINDING SITE FOR RESIDUE ZN A 228
04AC4SOFTWAREASP A:94 , HIS A:96 , ASP A:119 , HOH A:257 , GLU C:26 , ZN C:230BINDING SITE FOR RESIDUE ZN A 229
05AC5SOFTWAREGLU A:22 , GLN A:74BINDING SITE FOR RESIDUE ZN A 230
06AC6SOFTWAREVAL A:87 , TYR A:128 , PHE A:142 , PHE A:220BINDING SITE FOR RESIDUE MPD A 231
07AC7SOFTWAREILE A:159 , ARG A:189 , HOH A:246BINDING SITE FOR RESIDUE MPD A 232
08AC8SOFTWAREASP B:36 , HIS B:206 , GLU D:107BINDING SITE FOR RESIDUE ZN B 226
09AC9SOFTWAREASP B:135 , VAL B:139 , HIS B:141 , HOH B:251BINDING SITE FOR RESIDUE ZN B 227
10BC1SOFTWAREHIS B:96 , ASP B:119 , HOH B:252 , GLU D:26BINDING SITE FOR RESIDUE ZN B 228
11BC2SOFTWAREASP B:94 , HIS B:96 , HOH B:236 , GLU D:26BINDING SITE FOR RESIDUE ZN B 229
12BC3SOFTWARETHR B:21 , VAL B:87 , TYR B:128 , PHE B:142 , ILE B:208 , PHE B:220 , HOH B:250BINDING SITE FOR RESIDUE MPD B 230
13BC4SOFTWARETYR B:116 , LEU B:185 , ARG B:189BINDING SITE FOR RESIDUE MPD B 231
14BC5SOFTWAREASP A:55 , GLU A:107 , ASP C:36 , HIS C:206BINDING SITE FOR RESIDUE ZN C 226
15BC6SOFTWAREGLU A:170 , ASP C:135 , HIS C:141 , HOH C:262BINDING SITE FOR RESIDUE ZN C 227
16BC7SOFTWAREHIS C:96 , ASP C:119 , HOH C:237 , HOH C:268BINDING SITE FOR RESIDUE ZN C 228
17BC8SOFTWAREASP C:94 , ASP C:119BINDING SITE FOR RESIDUE ZN C 229
18BC9SOFTWAREASP A:94 , ZN A:229 , GLU C:22 , GLN C:74 , HOH C:270BINDING SITE FOR RESIDUE ZN C 230
19CC1SOFTWAREASP C:136BINDING SITE FOR RESIDUE ZN C 231
20CC2SOFTWARETYR C:128BINDING SITE FOR RESIDUE MPD C 232
21CC3SOFTWARETYR C:116 , LEU C:161 , ARG C:189 , ALA C:192 , HOH C:242BINDING SITE FOR RESIDUE MPD C 233
22CC4SOFTWAREGLU B:107 , ASP D:36 , HIS D:206BINDING SITE FOR RESIDUE ZN D 226
23CC5SOFTWAREASP D:135 , HIS D:141 , HOH D:251BINDING SITE FOR RESIDUE ZN D 227
24CC6SOFTWAREHIS D:96 , ASP D:119BINDING SITE FOR RESIDUE ZN D 228
25CC7SOFTWAREASP D:94 , ASP D:119 , HOH D:252 , HOH D:254BINDING SITE FOR RESIDUE ZN D 229
26CC8SOFTWAREASP B:94 , GLU D:22 , GLN D:74BINDING SITE FOR RESIDUE ZN D 230
27CC9SOFTWARETYR D:128 , PHE D:142 , PHE D:220BINDING SITE FOR RESIDUE MPD D 231
28DC1SOFTWAREILE D:101 , TYR D:116 , ILE D:159 , LEU D:188 , ARG D:189 , HOH D:253BINDING SITE FOR RESIDUE MPD D 232

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:9 -A:16
2A:151 -A:194
3B:9 -B:16
4B:151 -B:194
5C:9 -C:16
6C:151 -C:194
7D:9 -D:16
8D:151 -D:194

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Asp A:41 -Pro A:42
2Glu A:183 -Pro A:184
3Asp B:41 -Pro B:42
4Glu B:183 -Pro B:184
5Asp C:41 -Pro C:42
6Glu C:183 -Pro C:184
7Asp D:41 -Pro D:42
8Glu D:183 -Pro D:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A1Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3A1Z)

(-) Exons   (0, 0)

(no "Exon" information available for 3A1Z)

(-) 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:208
 aligned with Q9U556_BOMMO | Q9U556 from UniProtKB/TrEMBL  Length:243

    Alignment length:216
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234      
         Q9U556_BOMMO    25 KPCKLGDMQCLSSATEQFLEKTSKGIPQYDIWPIDPLVVTSLDVIAPSDAGIVIRFKNLNITGLKNQQISDFQMDTKAKTVLLKTKADLHIVGDIVIELTEQSKSFTGLYTADTNVIGAVRYGYNLKNDDNGVQHFEVQPETFTCESIGEPKITLSSDLSSALEKDSGNNSLEPDMEPLKTLRQAAICKIAEACYISVVHNIRASAKILPASSFFE 240
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh..hhhhh......eeeeeeeee......eeeeeeeeeeehhhhh....eeee....eeeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeeeeeee.....eeeee...eeeeee....eeeehhhhhhhhhhhhh--------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3a1z A   7 KPCKLGDMQCLSSATEQFLEKTSKGIPQYDIWPIDPLVVTSLDVIAPSDAGIVIRFKNLNITGLKNQQISDFQMDTKAKTVLLKTKADLHIVGDIVIELTEQSKSFTGLYTADTNVIGAVRYGYNLKNDDNGVQHFEVQPETFTCESIGEPKITLSSDLSSALEKDSG--------EPLKTLRQAAICKIAEACYISVVHNIRASAKILPASSFFE 222
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       | -      |186       196       206       216      
                                                                                                                                                                                                 174      183                                       


Chain B from PDB  Type:PROTEIN  Length:212
 aligned with Q9U556_BOMMO | Q9U556 from UniProtKB/TrEMBL  Length:243

    Alignment length:216
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234      
         Q9U556_BOMMO    25 KPCKLGDMQCLSSATEQFLEKTSKGIPQYDIWPIDPLVVTSLDVIAPSDAGIVIRFKNLNITGLKNQQISDFQMDTKAKTVLLKTKADLHIVGDIVIELTEQSKSFTGLYTADTNVIGAVRYGYNLKNDDNGVQHFEVQPETFTCESIGEPKITLSSDLSSALEKDSGNNSLEPDMEPLKTLRQAAICKIAEACYISVVHNIRASAKILPASSFFE 240
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhh..hhhhh......eeeeeeeeee..eeeeeeeeeeeeeehhhhh....eeee....eeeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeeeeeee.....eeeee...eeeeee....eeeehhhhhhhhhhhh..----....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3a1z B   7 KPCKLGDMQCLSSATEQFLEKTSKGIPQYDIWPIDPLVVTSLDVIAPSDAGIVIRFKNLNITGLKNQQISDFQMDTKAKTVLLKTKADLHIVGDIVIELTEQSKSFTGLYTADTNVIGAVRYGYNLKNDDNGVQHFEVQPETFTCESIGEPKITLSSDLSSALEKDSGN----PDMEPLKTLRQAAICKIAEACYISVVHNIRASAKILPASSFFE 222
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166        |-   |   186       196       206       216      
                                                                                                                                                                                                  175  180                                          


Chain C from PDB  Type:PROTEIN  Length:212
 aligned with Q9U556_BOMMO | Q9U556 from UniProtKB/TrEMBL  Length:243

    Alignment length:219
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232         
         Q9U556_BOMMO    23 LLKPCKLGDMQCLSSATEQFLEKTSKGIPQYDIWPIDPLVVTSLDVIAPSDAGIVIRFKNLNITGLKNQQISDFQMDTKAKTVLLKTKADLHIVGDIVIELTEQSKSFTGLYTADTNVIGAVRYGYNLKNDDNGVQHFEVQPETFTCESIGEPKITLSSDLSSALEKDSGNNSLEPDMEPLKTLRQAAICKIAEACYISVVHNIRASAKILPASSFFEN 241
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh...hhhhh......eeeeeeeeee..eeeeeeeeeeeeeehhhhh....eeee....eeeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeeeeeee.....eeeee...eeeeee....eeeehhhhhhhhhhhhh.-------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a1z C   5 LLKPCKLGDMQCLSSATEQFLEKTSKGIPQYDIWPIDPLVVTSLDVIAPSDAGIVIRFKNLNITGLKNQQISDFQMDTKAKTVLLKTKADLHIVGDIVIELTEQSKSFTGLYTADTNVIGAVRYGYNLKNDDNGVQHFEVQPETFTCESIGEPKITLSSDLSSALEKDSGN-------EPLKTLRQAAICKIAEACYISVVHNIRASAKILPASSFFEN 223
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174|      184       194       204       214         
                                                                                                                                                                                                    175     183                                        


Chain D from PDB  Type:PROTEIN  Length:209
 aligned with Q9U556_BOMMO | Q9U556 from UniProtKB/TrEMBL  Length:243

    Alignment length:216
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234      
         Q9U556_BOMMO    25 KPCKLGDMQCLSSATEQFLEKTSKGIPQYDIWPIDPLVVTSLDVIAPSDAGIVIRFKNLNITGLKNQQISDFQMDTKAKTVLLKTKADLHIVGDIVIELTEQSKSFTGLYTADTNVIGAVRYGYNLKNDDNGVQHFEVQPETFTCESIGEPKITLSSDLSSALEKDSGNNSLEPDMEPLKTLRQAAICKIAEACYISVVHNIRASAKILPASSFFE 240
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh..hhhhh......eeeeeeeee......eeeeeeeeeeehhhhheeeeeeee....eeeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeeeeeee.....eeeee...eeeeee....eeeehhhhhhhhhhhhh-------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3a1z D   7 KPCKLGDMQCLSSATEQFLEKTSKGIPQYDIWPIDPLVVTSLDVIAPSDAGIVIRFKNLNITGLKNQQISDFQMDTKAKTVLLKTKADLHIVGDIVIELTEQSKSFTGLYTADTNVIGAVRYGYNLKNDDNGVQHFEVQPETFTCESIGEPKITLSSDLSSALEKDSG-------MEPLKTLRQAAICKIAEACYISVVHNIRASAKILPASSFFE 222
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       | -     | 186       196       206       216      
                                                                                                                                                                                                 174     182
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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  (0, 0)

(no "SCOP Domain" information available for 3A1Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3A1Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A1Z)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q9U556_BOMMO | Q9U556)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  3a1z
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  Q9U556_BOMMO | Q9U556
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q9U556_BOMMO | Q9U556: 2rqf 3aos 3aot

(-) Related Entries Specified in the PDB File

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