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(-) Description

Title :  STRUCTURAL BASIS FOR THE IRON UPTAKE MECHANISM OF HELICOBACTER PYLORI FERRITIN
 
Authors :  K. H. Kim, K. J. Cho, J. H. Lee, H. J. Shin, I. S. Yang
Date :  07 Jan 08  (Deposition) - 13 Jan 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (4x)
Keywords :  Iron Storage, Metal-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. H. Kim, K. J. Cho, J. H. Lee, H. J. Shin, I. S. Yang
Structural Basis For The Iron Uptake Mechanism Of Helicobacter Pylori Ferritin
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FERRITIN
    ChainsA, B, C, D, E, F
    EC Number1.16.3.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETDUET
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificHELICOBACTER PYLORI
    Organism Taxid210
    StrainJ99

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (4x)ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric Unit (2, 17)
No.NameCountTypeFull Name
1FE14Ligand/IonFE (III) ION
2GOL3Ligand/IonGLYCEROL
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2GOL12Ligand/IonGLYCEROL

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:17 , GLU A:50 , HIS A:53 , ILE A:97 , GLN A:127 , GLU A:130 , FE A:1007BINDING SITE FOR RESIDUE FE A1006
02AC2SOFTWAREGLU A:50 , GLU A:94 , GLN A:127 , GLU A:130 , FE A:1006BINDING SITE FOR RESIDUE FE A1007
03AC3SOFTWAREGLU B:17 , GLU B:50 , HIS B:53 , ILE B:97 , GLN B:127 , GLU B:130 , FE B:1007BINDING SITE FOR RESIDUE FE B1006
04AC4SOFTWAREGLU B:50 , GLU B:94 , GLN B:127 , GLU B:130 , FE B:1006BINDING SITE FOR RESIDUE FE B1007
05AC5SOFTWAREGLU C:17 , GLU C:50 , HIS C:53 , GLN C:127 , GLU C:130 , FE C:1007BINDING SITE FOR RESIDUE FE C1006
06AC6SOFTWAREGLU C:50 , GLU C:94 , GLN C:127 , GLU C:130 , FE C:1006BINDING SITE FOR RESIDUE FE C1007
07AC7SOFTWAREGLU D:17 , GLU D:50 , HIS D:53 , GLN D:127 , GLU D:130 , FE D:1007BINDING SITE FOR RESIDUE FE D1006
08AC8SOFTWAREGLU D:50 , GLU D:94 , GLN D:127 , GLU D:130 , FE D:1006BINDING SITE FOR RESIDUE FE D1007
09AC9SOFTWAREGLU E:17 , GLU E:50 , HIS E:53 , GLN E:127 , GLU E:130 , FE E:1007BINDING SITE FOR RESIDUE FE E1006
10BC1SOFTWAREGLU E:50 , GLU E:94 , GLN E:127 , GLU E:130 , FE E:1006BINDING SITE FOR RESIDUE FE E1007
11BC2SOFTWAREGLU F:17 , GLU F:50 , HIS F:53 , GLN F:127 , GLU F:130 , FE F:1007BINDING SITE FOR RESIDUE FE F1006
12BC3SOFTWAREGLU F:50 , GLU F:94 , GLN F:127 , GLU F:130 , FE F:1006BINDING SITE FOR RESIDUE FE F1007
13BC4SOFTWAREMET A:18 , SER A:21 , ASN A:22 , TYR A:51 , MET F:18 , SER F:21 , ASN F:22BINDING SITE FOR RESIDUE GOL F1008
14BC5SOFTWAREMET B:18 , SER B:21 , ASN B:22 , HOH B:1070 , MET E:18 , ASN E:22 , TYR E:51BINDING SITE FOR RESIDUE GOL B1008
15BC6SOFTWAREMET C:18 , SER C:21 , ASN C:22 , HOH C:1035 , HOH C:1082 , MET D:18 , TYR D:51 , ILE D:73 , HOH D:1091BINDING SITE FOR RESIDUE GOL C1008

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BVK)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 6)

Asymmetric Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FERRITIN_LIKEPS50905 Ferritin-like diiron domain profile.FTN_HELPJ1-145
 
 
 
 
 
  6A:1-145
B:1-145
C:1-145
D:1-145
E:1-145
F:1-145
Biological Unit 1 (1, 24)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FERRITIN_LIKEPS50905 Ferritin-like diiron domain profile.FTN_HELPJ1-145
 
 
 
 
 
  24A:1-145
B:1-145
C:1-145
D:1-145
E:1-145
F:1-145

(-) Exons   (0, 0)

(no "Exon" information available for 3BVK)

(-) 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
 aligned with FTN_HELPJ | Q9ZLI1 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:172
                                  1                                                                                                                                                                     
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164  
           FTN_HELPJ      - ------MLSKDIIKLLNEQVNKEMNSSNLYMSMSSWCYTHSLDGAGLFLFDHAAEEYEHAKKLIIFLNENNVPVQLTSISAPEHKFEGLTQIFQKAYEHEQHISESINNIVDHAIKSKDHATFNFLQWYVAEQHEEEVLFKDILDKIELIGNENHGLYLADQYVKGIAKSRK  166
               SCOP domains d3bvka_ A: automated matches                                                                                                                                                 SCOP domains
               CATH domains 3bvkA00 A:1005-166  [code=1.20.1260.10, no name defined]                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------FERRITIN_LIKE  PDB: A:1-145 UniProt: 1-145                                                                                                       --------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3bvk A 1005 HHSQDPMLSKDIIKLLNEQVNKEMNSSNLYMSMSSWCYTHSLDGAGLFLFDHAAEEYEHAKKLIIFLNENNVPVQLTSISAPEHKFEGLTQIFQKAYEHEQHISESINNIVDHAIKSKDHATFNFLQWYVAEQHEEEVLFKDILDKIELIGNENHGLYLADQYVKGIAKSRK  166
                            ||||||   4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164  
                            ||||||                                                                                                                                                                      
                         1005|||||                                                                                                                                                                      
                          1004||||                                                                                                                                                                      
                           1003|||                                                                                                                                                                      
                            1002||                                                                                                                                                                      
                             1001|                                                                                                                                                                      
                                 0                                                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:172
 aligned with FTN_HELPJ | Q9ZLI1 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:172
                                  1                                                                                                                                                                     
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164  
           FTN_HELPJ      - ------MLSKDIIKLLNEQVNKEMNSSNLYMSMSSWCYTHSLDGAGLFLFDHAAEEYEHAKKLIIFLNENNVPVQLTSISAPEHKFEGLTQIFQKAYEHEQHISESINNIVDHAIKSKDHATFNFLQWYVAEQHEEEVLFKDILDKIELIGNENHGLYLADQYVKGIAKSRK  166
               SCOP domains d3bvkb_ B: automated matches                                                                                                                                                 SCOP domains
               CATH domains 3bvkB00 B:1005-166  [code=1.20.1260.10, no name defined]                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------FERRITIN_LIKE  PDB: B:1-145 UniProt: 1-145                                                                                                       --------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3bvk B 1005 HHSQDPMLSKDIIKLLNEQVNKEMNSSNLYMSMSSWCYTHSLDGAGLFLFDHAAEEYEHAKKLIIFLNENNVPVQLTSISAPEHKFEGLTQIFQKAYEHEQHISESINNIVDHAIKSKDHATFNFLQWYVAEQHEEEVLFKDILDKIELIGNENHGLYLADQYVKGIAKSRK  166
                            ||||||   4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164  
                         1005|||||                                                                                                                                                                      
                          1004||||                                                                                                                                                                      
                           1003|||                                                                                                                                                                      
                            1002||                                                                                                                                                                      
                             1001|                                                                                                                                                                      
                                 0                                                                                                                                                                      

Chain C from PDB  Type:PROTEIN  Length:172
 aligned with FTN_HELPJ | Q9ZLI1 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:172
                                  1                                                                                                                                                                     
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164  
           FTN_HELPJ      - ------MLSKDIIKLLNEQVNKEMNSSNLYMSMSSWCYTHSLDGAGLFLFDHAAEEYEHAKKLIIFLNENNVPVQLTSISAPEHKFEGLTQIFQKAYEHEQHISESINNIVDHAIKSKDHATFNFLQWYVAEQHEEEVLFKDILDKIELIGNENHGLYLADQYVKGIAKSRK  166
               SCOP domains d3bvkc_ C: automated matches                                                                                                                                                 SCOP domains
               CATH domains 3bvkC00 C:1005-166  [code=1.20.1260.10, no name defined]                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------FERRITIN_LIKE  PDB: C:1-145 UniProt: 1-145                                                                                                       --------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3bvk C 1005 HHSQDPMLSKDIIKLLNEQVNKEMNSSNLYMSMSSWCYTHSLDGAGLFLFDHAAEEYEHAKKLIIFLNENNVPVQLTSISAPEHKFEGLTQIFQKAYEHEQHISESINNIVDHAIKSKDHATFNFLQWYVAEQHEEEVLFKDILDKIELIGNENHGLYLADQYVKGIAKSRK  166
                            ||||||   4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164  
                         1005|||||                                                                                                                                                                      
                          1004||||                                                                                                                                                                      
                           1003|||                                                                                                                                                                      
                            1002||                                                                                                                                                                      
                             1001|                                                                                                                                                                      
                                 0                                                                                                                                                                      

Chain D from PDB  Type:PROTEIN  Length:172
 aligned with FTN_HELPJ | Q9ZLI1 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:172
                                  1                                                                                                                                                                     
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164  
           FTN_HELPJ      - ------MLSKDIIKLLNEQVNKEMNSSNLYMSMSSWCYTHSLDGAGLFLFDHAAEEYEHAKKLIIFLNENNVPVQLTSISAPEHKFEGLTQIFQKAYEHEQHISESINNIVDHAIKSKDHATFNFLQWYVAEQHEEEVLFKDILDKIELIGNENHGLYLADQYVKGIAKSRK  166
               SCOP domains d3bvkd_ D: automated matches                                                                                                                                                 SCOP domains
               CATH domains 3bvkD00 D:1005-166  [code=1.20.1260.10, no name defined]                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------FERRITIN_LIKE  PDB: D:1-145 UniProt: 1-145                                                                                                       --------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3bvk D 1005 HHSQDPMLSKDIIKLLNEQVNKEMNSSNLYMSMSSWCYTHSLDGAGLFLFDHAAEEYEHAKKLIIFLNENNVPVQLTSISAPEHKFEGLTQIFQKAYEHEQHISESINNIVDHAIKSKDHATFNFLQWYVAEQHEEEVLFKDILDKIELIGNENHGLYLADQYVKGIAKSRK  166
                            ||||||   4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164  
                         1005|||||                                                                                                                                                                      
                          1004||||                                                                                                                                                                      
                           1003|||                                                                                                                                                                      
                            1002||                                                                                                                                                                      
                             1001|                                                                                                                                                                      
                                 0                                                                                                                                                                      

Chain E from PDB  Type:PROTEIN  Length:172
 aligned with FTN_HELPJ | Q9ZLI1 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:172
                                  1                                                                                                                                                                     
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164  
           FTN_HELPJ      - ------MLSKDIIKLLNEQVNKEMNSSNLYMSMSSWCYTHSLDGAGLFLFDHAAEEYEHAKKLIIFLNENNVPVQLTSISAPEHKFEGLTQIFQKAYEHEQHISESINNIVDHAIKSKDHATFNFLQWYVAEQHEEEVLFKDILDKIELIGNENHGLYLADQYVKGIAKSRK  166
               SCOP domains d3bvke_ E: automated matches                                                                                                                                                 SCOP domains
               CATH domains 3bvkE00 E:1005-166  [code=1.20.1260.10, no name defined]                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------FERRITIN_LIKE  PDB: E:1-145 UniProt: 1-145                                                                                                       --------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3bvk E 1005 HHSQDPMLSKDIIKLLNEQVNKEMNSSNLYMSMSSWCYTHSLDGAGLFLFDHAAEEYEHAKKLIIFLNENNVPVQLTSISAPEHKFEGLTQIFQKAYEHEQHISESINNIVDHAIKSKDHATFNFLQWYVAEQHEEEVLFKDILDKIELIGNENHGLYLADQYVKGIAKSRK  166
                            ||||||   4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164  
                         1005|||||                                                                                                                                                                      
                          1004||||                                                                                                                                                                      
                           1003|||                                                                                                                                                                      
                            1002||                                                                                                                                                                      
                             1001|                                                                                                                                                                      
                                 0                                                                                                                                                                      

Chain F from PDB  Type:PROTEIN  Length:172
 aligned with FTN_HELPJ | Q9ZLI1 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:172
                                  1                                                                                                                                                                     
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164  
           FTN_HELPJ      - ------MLSKDIIKLLNEQVNKEMNSSNLYMSMSSWCYTHSLDGAGLFLFDHAAEEYEHAKKLIIFLNENNVPVQLTSISAPEHKFEGLTQIFQKAYEHEQHISESINNIVDHAIKSKDHATFNFLQWYVAEQHEEEVLFKDILDKIELIGNENHGLYLADQYVKGIAKSRK  166
               SCOP domains d3bvkf_ F: automated matches                                                                                                                                                 SCOP domains
               CATH domains 3bvkF00 F:1005-166  [code=1.20.1260.10, no name defined]                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------FERRITIN_LIKE  PDB: F:1-145 UniProt: 1-145                                                                                                       --------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3bvk F 1005 HHSQDPMLSKDIIKLLNEQVNKEMNSSNLYMSMSSWCYTHSLDGAGLFLFDHAAEEYEHAKKLIIFLNENNVPVQLTSISAPEHKFEGLTQIFQKAYEHEQHISESINNIVDHAIKSKDHATFNFLQWYVAEQHEEEVLFKDILDKIELIGNENHGLYLADQYVKGIAKSRK  166
                            ||||||   4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164  
                         1005|||||                                                                                                                                                                      
                          1004||||                                                                                                                                                                      
                           1003|||                                                                                                                                                                      
                            1002||                                                                                                                                                                      
                             1001|                                                                                                                                                                      
                                 0                                                                                                                                                                      

   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  (1, 6)

Asymmetric Unit

(-) CATH Domains  (1, 6)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (FTN_HELPJ | Q9ZLI1)
molecular function
    GO:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0006879    cellular iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
    GO:0006826    iron ion transport    The directed movement of iron (Fe) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FTN_HELPJ | Q9ZLI13bve 3bvf 3bvi 3bvl 3egm 5c6f

(-) Related Entries Specified in the PDB File

3bve 3bvf 3bvi 3bvl