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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NOVEL COMPLEX FORMED BETWEEN ZINC 2-GLYCOPROTEIN (ZAG) AND PROLACTIN INDUCIBLE PROTEIN (PIP) FROM HUMAN SEMINAL PLASMA
 
Authors :  M. I. Hassan, S. Bilgrami, V. Kumar, N. Singh, S. Yadav, P. Kaur, T. P. Sin
Date :  04 Oct 08  (Deposition) - 28 Oct 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.23
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Major Histocompatibility Complex, Protein-Protein Complex, Prolactin Inducible Protein, Zinc 2-Glycoprotein, Zag-Pip Complex, Glycoprotein, Pyrrolidone Carboxylic Acid, Secreted, Actin-Binding, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. I. Hassan, S. Bilgrami, V. Kumar, N. Singh, S. Yadav, P. Kaur, T. P. Singh
Crystal Structure Of The Novel Complex Formed Between Zinc Alpha2-Glycoprotein (Zag) And Prolactin-Inducible Protein (Pip) From Human Seminal Plasma
J. Mol. Biol. V. 384 663 2008
PubMed-ID: 18930737  |  Reference-DOI: 10.1016/J.JMB.2008.09.072

(-) Compounds

Molecule 1 - ZINC-ALPHA-2-GLYCOPROTEIN
    ChainsA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsSEMINAL FLUID
    SynonymZN-ALPHA-2-GLYCOPROTEIN, ZN-ALPHA-2-GP
 
Molecule 2 - PROLACTIN-INDUCIBLE PROTEIN
    ChainsB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsSEMINAL FLUID
    SynonymPROLACTIN-INDUCED PROTEIN, SECRETORY ACTIN-BINDING PROTEIN, SABP, GROSS CYSTIC DISEASE FLUID PROTEIN 15, GCDFP-15, GP17

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 12)

Asymmetric Unit (7, 12)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CO31Ligand/IonCARBONATE ION
3MAN2Ligand/IonALPHA-D-MANNOSE
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
5NDG2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6P6G1Ligand/IonHEXAETHYLENE GLYCOL
7PCA1Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 1 (7, 8)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CO31Ligand/IonCARBONATE ION
3MAN1Ligand/IonALPHA-D-MANNOSE
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
5NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6P6G1Ligand/IonHEXAETHYLENE GLYCOL
7PCA1Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CO3-1Ligand/IonCARBONATE ION
3MAN1Ligand/IonALPHA-D-MANNOSE
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
5NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6P6G-1Ligand/IonHEXAETHYLENE GLYCOL
7PCA-1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN B:21 , GLN B:51 , ASN B:77 , NAG B:301BINDING SITE FOR RESIDUE NDG B 300
02AC2SOFTWARENDG B:300 , BMA B:302BINDING SITE FOR RESIDUE NAG B 301
03AC3SOFTWARENAG B:301 , MAN B:303BINDING SITE FOR RESIDUE BMA B 302
04AC4SOFTWAREBMA B:302BINDING SITE FOR RESIDUE MAN B 303
05AC5SOFTWAREASP A:209 , HIS A:236 , ASN A:239 , NAG A:321BINDING SITE FOR RESIDUE NAG A 320
06AC6SOFTWARETYR A:208 , ASP A:209 , NAG A:320 , BMA A:322 , MAN A:327BINDING SITE FOR RESIDUE NAG A 321
07AC7SOFTWARETYR A:208 , NAG A:321 , MAN A:327BINDING SITE FOR RESIDUE BMA A 322
08AC8SOFTWARELYS A:204 , LEU A:206 , NAG A:321 , BMA A:322 , NDG A:328BINDING SITE FOR RESIDUE MAN A 327
09AC9SOFTWARELYS A:204 , MAN A:327BINDING SITE FOR RESIDUE NDG A 328
10BC1SOFTWAREHIS A:236 , ASN A:237 , GLY A:238 , GLN B:51 , GLY B:52BINDING SITE FOR RESIDUE CO3 A 688
11BC2SOFTWAREARG A:73 , PHE A:77 , TRP A:115 , TYR A:117BINDING SITE FOR RESIDUE P6G A 701

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:103 -A:166
2A:205 -A:260
3B:37 -B:63
4B:61 -B:95

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ile A:131 -Pro A:132
2Tyr A:211 -Pro A:212

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ES6)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.ZA2G_HUMAN278-284  1A:258-264
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.ZA2G_HUMAN278-284  1A:258-264
Biological Unit 2 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.ZA2G_HUMAN278-284  0-

(-) Exons   (8, 8)

Asymmetric Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002910091ENSE00001047638chr7:142829170-142829304135PIP_HUMAN1-32321B:1-44
1.2ENST000002910092ENSE00001047639chr7:142832287-142832392106PIP_HUMAN32-67361B:4-3936
1.3ENST000002910093ENSE00001047640chr7:142836168-142836282115PIP_HUMAN68-106391B:40-7839
1.4ENST000002910094ENSE00001047636chr7:142836611-142836839229PIP_HUMAN106-146411B:78-11841

2.1aENST000002924011aENSE00001907842chr7:99573780-99573568213ZA2G_HUMAN1-26261A:1-66
2.2bENST000002924012bENSE00001055051chr7:99569629-99569369261ZA2G_HUMAN26-113881A:6-9388
2.4bENST000002924014bENSE00001801964chr7:99566053-99565778276ZA2G_HUMAN113-205931A:93-18593
2.4hENST000002924014hENSE00001820318chr7:99564909-99564353557ZA2G_HUMAN205-298941A:185-27793

(-) 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:277
 aligned with ZA2G_HUMAN | P25311 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:277
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       
           ZA2G_HUMAN    21 QENQDGRYSLTYIYTGLSKHVEDVPAFQALGSLNDLQFFRYNSKDRKSQPMGLWRQVEGMEDWKQDSQLQKAREDIFMETLKDIVEYYNDSNGSHVLQGRFGCEIENNRSSGAFWKYYYDGKDYIEFNKEIPAWVPFDPAAQITKQKWEAEPVYVQRAKAYLEEECPATLRKYLKYSKNILDRQDPPSVVVTSHQAPGEKKKLKCLAYDFYPGKIDVHWTRAGEVQEPELRGDVLHNGNGTYQSWVVVAVPPQDTAPYSCHVQHSSLAQPLVVPWEA 297
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----3es6A01 A:6-183 Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1                                                                                       3es6A02 A:184-273 Immunoglobulins                                                         ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee.........eeeeeee..eeeeeee......ee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeee..eeeeeeeeeee..eeeeeee....eeee...hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee.....eeeeeeeeee....eeeeeee..eee...eeeeeee....eeeeeeeeee.......eeeeeee......eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------- PROSITE
           Transcript 2 (1) 2.1a  --------------------------------------------------------------------------------------Exon 2.4b  PDB: A:93-185 UniProt: 113-205                                                    -------------------------------------------------------------------------------------------- Transcript 2 (1)
           Transcript 2 (2) -----Exon 2.2b  PDB: A:6-93 UniProt: 26-113                                                  -------------------------------------------------------------------------------------------Exon 2.4h  PDB: A:185-277 UniProt: 205-298 [INCOMPLETE]                                       Transcript 2 (2)
                 3es6 A   1 xENQDGRYSLTYIYTGLSKHVEDVPAFQALGSLNDLQFFRYNSKDRKSQPMGLWRQVEGMEDWKQDSQLQKAREDIFMETLKDIVEYYNDSNGSHVLQGRFGCEIENNRSSGAFWKYYYDGKDYIEFNKEIPAWVPFDPAAQITKQKWEAEPVYVQRAKAYLEEECPATLRKYLKYSKNILDRQDPPSVVVTSHQAPGEKKKLKCLAYDFYPGKIDVHWTRAGEVQEPELRGDVLHNGNGTYQSWVVVAVPPQDTAPYSCHVQHSSLAQPLVVPWEA 277
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       
                            1-PCA                                                                                                                                                                                                                                                                                

Chain B from PDB  Type:PROTEIN  Length:118
 aligned with PIP_HUMAN | P12273 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:118
                                    38        48        58        68        78        88        98       108       118       128       138        
            PIP_HUMAN    29 QDNTRKIIIKNFDIPKSVRPNDEVTAVLAVQTELKECMVVKTYLISSIPLQGAFNYKYTACLCDDNPKTFYWDFYTNRTVQIAAVVDVIRELGICPDDAAVIPIKNNRFYTIEILKVE 146
               SCOP domains d3es6b1 B:1-118 Prolactin-inducible protein, PIP                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee......ee.....eeeeeeeee.....eeeeeeeee.....hhhhheeeeee.....eeeeeee.....eeeeeeeee......hhhhh........eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1 -----------------------------------Exon 1.3  PDB: B:40-78 UniProt: 68-106 ---------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.2  PDB: B:4-39 UniProt: 32-67--------------------------------------Exon 1.4  PDB: B:78-118 UniProt: 106-146  Transcript 1 (2)
                 3es6 B   1 QDNTRKIIIKNFDIPKSVRPNDEVTAVLAVQTELKECMVVKTYLISSIPLQGAFNYKYTACLCDDNPKTFYWDFYTNRTVQIAAVVDVIRELGICPDDAAVIPIKNNRFYTIEILKVE 118
                                    10        20        30        40        50        60        70        80        90       100       110        

   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, 1)

Asymmetric Unit

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ES6)

(-) Gene Ontology  (30, 38)

Asymmetric Unit(hide GO term definitions)
Chain A   (ZA2G_HUMAN | P25311)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
    GO:0042605    peptide antigen binding    Interacting selectively and non-covalently with an antigen peptide.
    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:0008320    protein transmembrane transporter activity    Enables the transfer of a protein from one side of a membrane to the other.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0019882    antigen processing and presentation    The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
    GO:0002474    antigen processing and presentation of peptide antigen via MHC class I    The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0001580    detection of chemical stimulus involved in sensory perception of bitter taste    The series of events required for a bitter taste stimulus to be received and converted to a molecular signal.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0071806    protein transmembrane transport    The directed movement of a protein across a membrane by means of some agent such as a transporter or pore.
    GO:0001895    retina homeostasis    A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
cellular component
    GO:0042612    MHC class I protein complex    A transmembrane protein complex composed of a MHC class I alpha chain and an invariant beta2-microglobin chain, and with or without a bound peptide antigen. Class I here refers to classical class I molecules.
    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: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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain B   (PIP_HUMAN | P12273)
molecular function
    GO:0019864    IgG binding    Interacting selectively and non-covalently with an immunoglobulin of an IgG isotype.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    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:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
biological process
    GO:0001580    detection of chemical stimulus involved in sensory perception of bitter taste    The series of events required for a bitter taste stimulus to be received and converted to a molecular signal.
    GO:0070233    negative regulation of T cell apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of T cell death by apoptotic process.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0002682    regulation of immune system process    Any process that modulates the frequency, rate, or extent of an immune system process.
    GO:0001895    retina homeostasis    A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
cellular component
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ZA2G_HUMAN | P253111t7v 1t7w 1t7x 1t7y 1t7z 1t80 1zag

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3ES6)