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(-) Description

Title :  CRYSTAL STRUCTURE OF ERP46 TRX2 IN A COMPLEX WITH PRX4 C-TERM
 
Authors :  K. Inaba, M. Suzuki, R. Kojima
Date :  13 Aug 13  (Deposition) - 25 Jun 14  (Release) - 25 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.92
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Pdi Family Member, Thioredoxin Domain, Protein Disulfide Isomerase, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Kojima, M. Okumura, S. Masui, S. Kanemura, M. Inoue, M. Saiki, H. Yamaguchi, T. Hikima, M. Suzuki, S. Akiyama, K. Inaba
Radically Different Thioredoxin Domain Arrangement Of Erp46 An Efficient Disulfide Bond Introducer Of The Mammalian Pdi Family
Structure V. 22 431 2014
PubMed-ID: 24462249  |  Reference-DOI: 10.1016/J.STR.2013.12.013

(-) Compounds

Molecule 1 - THIOREDOXIN DOMAIN-CONTAINING PROTEIN 5
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPOPTG
    Expression System StrainC41(DE3)RIPL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentTRX2 DOMAIN, UNP RESIDUES 190-298
    GeneTLP46
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymERP46, ENDOPLASMIC RETICULUM RESIDENT PROTEIN 46, ER PROTEIN 46, THIOREDOXIN-LIKE PROTEIN P46
 
Molecule 2 - PEROXIREDOXIN-4
    ChainsC, D
    EngineeredYES
    FragmentC-TERM DOMAIN, UNP RESIDUES 244-263
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsCHEMICAL SYNTHESIS
    SynonymPRX4
    SyntheticYES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:280 , ASP B:207 , ARG B:269 , ASP B:270 , THR B:297 , GLU B:298 , HOH B:523 , HOH B:592 , HIS C:294BINDING SITE FOR RESIDUE GOL B 301

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:217 -C:298
2A:247 -A:254
3B:217 -D:298
4B:247 -B:254

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:262 -Pro A:263
2Tyr B:262 -Pro B:263

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.TXND5_HUMAN81-99
209-227
 
342-360
  2-
A:209-227
B:209-227
-
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.TXND5_HUMAN81-99
209-227
 
342-360
  1-
A:209-227
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.TXND5_HUMAN81-99
209-227
 
342-360
  1-
-
B:209-227
-

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003797571ENSE00001482400chr6:7911047-7910747301TXND5_HUMAN1-88880--
1.3ENST000003797573ENSE00002035816chr6:7904956-7904807150TXND5_HUMAN88-138510--
1.4bENST000003797574bENSE00002030712chr6:7899914-7899809106TXND5_HUMAN138-173360--
1.5bENST000003797575bENSE00002020031chr6:7895435-789533997TXND5_HUMAN174-206332A:187-206
B:187-206
20
20
1.6ENST000003797576ENSE00002062288chr6:7891969-7891854116TXND5_HUMAN206-244392A:206-244
B:206-244
39
39
1.7ENST000003797577ENSE00002051337chr6:7889814-788972887TXND5_HUMAN245-273292A:245-273
B:245-273
29
29
1.8cENST000003797578cENSE00002072823chr6:7889081-7888938144TXND5_HUMAN274-321482A:274-295
B:274-298
22
25
1.9ENST000003797579ENSE00002061487chr6:7886276-788619483TXND5_HUMAN322-349280--
1.10ENST0000037975710ENSE00002026226chr6:7884721-7884592130TXND5_HUMAN349-392440--
1.11cENST0000037975711cENSE00001964269chr6:7883499-78817501750TXND5_HUMAN393-432400--

(-) 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:109
 aligned with TXND5_HUMAN | Q8NBS9 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:109
                                   196       206       216       226       236       246       256       266       276       286         
          TXND5_HUMAN   187 LKQGLYELSASNFELHVAQGDHFIKFFAPWCGHCKALAPTWEQLALGLEHSETVKIGKVDCTQHYELCSGNQVRGYPTLLWFRDGKKVDQYKGKRDLESLREYVESQLQ 295
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...hhhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhh...ee.eeeeee..eeeee.....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------THIOREDOXIN_1      -------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5b           --------------------------------------Exon 1.7  PDB: A:245-273     Exon 1.8c [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) -------------------Exon 1.6  PDB: A:206-244               --------------------------------------------------- Transcript 1 (2)
                 3wgx A 187 SHMGLYELSASNFELHVAQGDHFIKFFAPWCGHAKALAPTWEQLALGLEHSETVKIGKVDCTQHYELCSGNQVRGYPTLLWFRDGKKVDQYKGKRDLESLREYVESQLQ 295
                                   196       206       216       226       236       246       256       266       276       286         

Chain B from PDB  Type:PROTEIN  Length:112
 aligned with TXND5_HUMAN | Q8NBS9 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:112
                                   196       206       216       226       236       246       256       266       276       286       296  
          TXND5_HUMAN   187 LKQGLYELSASNFELHVAQGDHFIKFFAPWCGHCKALAPTWEQLALGLEHSETVKIGKVDCTQHYELCSGNQVRGYPTLLWFRDGKKVDQYKGKRDLESLREYVESQLQRTE 298
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...hhhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhh.....eeeeeee...hhhhhhh....ee.eeeeee..eeeee.....hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------THIOREDOXIN_1      ----------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5b           --------------------------------------Exon 1.7  PDB: B:245-273     Exon 1.8c  PDB: B:274-298 Transcript 1 (1)
           Transcript 1 (2) -------------------Exon 1.6  PDB: B:206-244               ------------------------------------------------------ Transcript 1 (2)
                 3wgx B 187 SHMGLYELSASNFELHVAQGDHFIKFFAPWCGHAKALAPTWEQLALGLEHSETVKIGKVDCTQHYELCSGNQVRGYPTLLWFRDGKKVDQYKGKRDLESLREYVESQLQRTE 298
                                   196       206       216       226       236       246       256       266       276       286       296  

Chain C from PDB  Type:PROTEIN  Length:7
 aligned with PRDX4_MOUSE | O08807 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:7
          PRDX4_MOUSE   244 HGEVCPA 250
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....ee. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 3wgx C 294 HGEVCPA 300

Chain D from PDB  Type:PROTEIN  Length:6
 aligned with PRDX4_MOUSE | O08807 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:6
          PRDX4_MOUSE   245 GEVCPA 250
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...ee. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 3wgx D 295 GEVCPA 300

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 36)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TXND5_HUMAN | Q8NBS9)
molecular function
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0003756    protein disulfide isomerase activity    Catalysis of the rearrangement of both intrachain and interchain disulfide bonds in proteins.
biological process
    GO:0043277    apoptotic cell clearance    The recognition and removal of an apoptotic cell by a neighboring cell or by a phagocyte.
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0034976    response to endoplasmic reticulum stress    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0043202    lysosomal lumen    The volume enclosed within the lysosomal membrane.

Chain C,D   (PRDX4_MOUSE | O08807)
molecular function
    GO:0016209    antioxidant activity    Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
    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.
    GO:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
    GO:0051920    peroxiredoxin activity    Catalysis of the reaction: 2 R'-SH + ROOH = R'-S-S-R' + H2O + ROH.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0019471    4-hydroxyproline metabolic process    The chemical reactions and pathways involving 4-hydroxyproline, C5H9NO3, a derivative of the amino acid proline. The presence of hydroxyproline is essential to produce stable triple helical tropocollagen, hence the problems caused by ascorbate deficiency in scurvy. This unusual amino acid is also present in considerable amounts in the major glycoprotein of primary plant cell walls.
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    GO:0008584    male gonad development    The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
    GO:2000255    negative regulation of male germ cell proliferation    Any process that stops, prevents or reduces the frequency, rate or extent of male germ cell proliferation.
    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.
    GO:0022417    protein maturation by protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that results in the attainment of the full functional capacity of a protein.
    GO:0072593    reactive oxygen species metabolic process    The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005790    smooth endoplasmic reticulum    The smooth endoplasmic reticulum (smooth ER or SER) has no ribosomes attached to it. The smooth ER is the recipient of the proteins synthesized in the rough ER. Those proteins to be exported are passed to the Golgi complex, the resident proteins are returned to the rough ER and the lysosomal proteins after phosphorylation of their mannose residues are passed to the lysosomes. Glycosylation of the glycoproteins also continues. The smooth ER is the site of synthesis of lipids, including the phospholipids. The membranes of the smooth ER also contain enzymes that catalyze a series of reactions to detoxify both lipid-soluble drugs and harmful products of metabolism. Large quantities of certain compounds such as phenobarbital cause an increase in the amount of the smooth ER.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PRDX4_MOUSE | O088073vwu 3vwv 3w8j
        TXND5_HUMAN | Q8NBS92diz 3uj1 3uvt 3wgd 3wge

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3WGX)