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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN GGA1 GAT DOMAIN COMPLEXED WITH THE GAT-BINDING DOMAIN OF RABAPTIN5
 
Authors :  G. Zhu, X. C. Zhang
Date :  13 Aug 04  (Deposition) - 12 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.41
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Rabaptin5, Gga Protein, Gat Domain, Intracellular Trafficking, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Zhu, P. Zhai, X. He, N. Wakeham, K. Rodgers, G. Li, J. Tang, X. C. Zhang
Crystal Structure Of Human Gga1 Gat Domain Complexed With The Gat-Binding Domain Of Rabaptin5
Embo J. V. 23 3909 2004
PubMed-ID: 15457209  |  Reference-DOI: DOI:10.1038/SJ.EMBOJ.7600411
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX6P-1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneGGA1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGOLGI-LOCALIZED, GAMMA EAR-CONTAINING, ARF- BINDING PROTEIN 1, GAMMA-ADAPTIN RELATED PROTEIN 1
 
Molecule 2 - RAB GTPASE BINDING EFFECTOR PROTEIN 1
    ChainsB, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET11A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneRABEP1, RABPT5, RABPT5A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRABAPTIN-5, RABAPTIN-5ALPHA, RABAPTIN-4

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1DTT2Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
2SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN B:614 , SER B:618 , LYS B:621BINDING SITE FOR RESIDUE SO4 B 391
2AC2SOFTWAREHOH C:440 , HOH C:461 , GLN C:614 , SER C:618 , LYS C:621BINDING SITE FOR RESIDUE SO4 C 392
3AC3SOFTWAREPHE B:584 , SER B:588 , PHE C:584 , SER C:588 , SER C:589BINDING SITE FOR RESIDUE DTT C 394
4AC4SOFTWAREGLN B:595 , LEU B:599 , LEU B:631 , SER B:634 , ILE C:596 , LEU C:599 , SER C:634BINDING SITE FOR RESIDUE DTT B 395

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X79)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X79)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_028106E640GRABE1_HUMANPolymorphism3026099B/CE640G

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X79)

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003436321aENSE00001813421chr22:38004482-38004910429GGA1_HUMAN1-15150--
1.7cENST000003436327cENSE00002140158chr22:38010197-3801028185GGA1_HUMAN15-43290--
1.8aENST000003436328aENSE00001612880chr22:38012929-3801300476GGA1_HUMAN43-68260--
1.9cENST000003436329cENSE00001683976chr22:38014455-3801455399GGA1_HUMAN69-101330--
1.10fENST0000034363210fENSE00000880168chr22:38016245-38016368124GGA1_HUMAN102-143420--
1.11bENST0000034363211bENSE00000880169chr22:38016820-38016920101GGA1_HUMAN143-176340--
1.12cENST0000034363212cENSE00000653934chr22:38017623-3801770381GGA1_HUMAN177-203270--
1.13ENST0000034363213ENSE00000880172chr22:38019334-38019474141GGA1_HUMAN204-250471A:211-250 (gaps)40
1.14bENST0000034363214bENSE00000880174chr22:38019559-3801964082GGA1_HUMAN251-278281A:251-27828
1.14eENST0000034363214eENSE00001286815chr22:38020976-38021083108GGA1_HUMAN278-314371A:278-29922
1.15aENST0000034363215aENSE00000653938chr22:38021804-38021956153GGA1_HUMAN314-365520--
1.16ENST0000034363216ENSE00000653944chr22:38025469-3802553365GGA1_HUMAN365-386220--
1.17aENST0000034363217aENSE00000653945chr22:38026005-38026177173GGA1_HUMAN387-444580--
1.18bENST0000034363218bENSE00000653946chr22:38026910-38027106197GGA1_HUMAN444-510670--
1.19ENST0000034363219ENSE00000653947chr22:38028003-38028172170GGA1_HUMAN510-566570--
1.20ENST0000034363220ENSE00000653948chr22:38028412-38028522111GGA1_HUMAN567-603370--
1.21dENST0000034363221dENSE00001823052chr22:38028608-38029571964GGA1_HUMAN604-639360--

(-) Sequences/Alignments

Asymmetric/Biological 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:82
 aligned with GGA1_HUMAN | Q9UJY5 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:89
                                   220       230       240       250       260       270       280       290         
           GGA1_HUMAN   211 ISKRVNAIEEVNNNVKLLTEMVMSHSQGGAAAGSSEDLMKELYQRCERMRPTLFRLASDTEDNDEALAEILQANDNLTQVINLYKQLVR 299
               SCOP domains d1x79a_ A: ADP-ribosylatio       n factor binding protein Gga1                            SCOP domains
               CATH domains 1x79A00 A:211-299  [code=1       .20.58.160, no name defined]                             CATH domains
               Pfam domains GAT-1x79A01 A:211-299                                                                     Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh..-------hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.13  PDB: A:211-250 (gaps)        Exon 1.14b  PDB: A:251-278  --------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------Exon 1.14e             Transcript 1 (2)
                 1x79 A 211 ISKRVNAIEEVNNNVKLLTEMVMSHS-------SSEDLMKELYQRCERMRPTLFRLASDTEDNDEALAEILQANDNLTQVINLYKQLVR 299
                                   220       230     |   -   |   250       260       270       280       290         
                                                   236     244                                                       

Chain B from PDB  Type:PROTEIN  Length:90
 aligned with RABE1_HUMAN | Q15276 from UniProtKB/Swiss-Prot  Length:862

    Alignment length:90
                                   561       571       581       591       601       611       621       631       641
          RABE1_HUMAN   552 ETRDQVKKLQLMLRQANDQLEKTMKDKQELEDFIKQSSEDSSHQISALVLRAQASEILLEELQQGLSQAKRDVQEQMAVLMQSREQVSEE 641
               SCOP domains d1x79b_ B: Rabaptin-5                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------G- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 1x79 B 552 ETRDQVKKLQLMLRQANDQLEKTMKDKQELEDFIKQSSEDSSHQISALVLRAQASEILLEELQQGLSQAKRDVQEQMAVLMQSREQVSEE 641
                                   561       571       581       591       601       611       621       631       641

Chain C from PDB  Type:PROTEIN  Length:88
 aligned with RABE1_HUMAN | Q15276 from UniProtKB/Swiss-Prot  Length:862

    Alignment length:88
                                   562       572       582       592       602       612       622       632        
          RABE1_HUMAN   553 TRDQVKKLQLMLRQANDQLEKTMKDKQELEDFIKQSSEDSSHQISALVLRAQASEILLEELQQGLSQAKRDVQEQMAVLMQSREQVSE 640
               SCOP domains d1x79c_ C: Rabaptin-5                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Rabaptin-1x79C03 C:553-596                  ---------------Rab5-bind-1x79C01 C:612-640   Pfam domains (1)
           Pfam domains (2) Rabaptin-1x79C04 C:553-596                  ---------------Rab5-bind-1x79C02 C:612-640   Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------G SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 1x79 C 553 TRDQVKKLQLMLRQANDQLEKTMKDKQELEDFIKQSSEDSSHQISALVLRAQASEILLEELQQGLSQAKRDVQEQMAVLMQSREQVSE 640
                                   562       572       582       592       602       612       622       632        

   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  (2, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (3, 5)

Asymmetric/Biological Unit
(-)
Clan: TPR (230)

(-) Gene Ontology  (29, 35)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GGA1_HUMAN | Q9UJY5)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    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).
biological process
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0006886    intracellular protein transport    The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
    GO:0045732    positive regulation of protein catabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:1901998    toxin transport    The directed movement of a toxin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0030131    clathrin adaptor complex    A membrane coat adaptor complex that links clathrin to a membrane.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

Chain B,C   (RABE1_HUMAN | Q15276)
molecular function
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0061025    membrane fusion    The membrane organization process that joins two lipid bilayers to form a single membrane.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0030139    endocytic vesicle    A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0055037    recycling endosome    An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GGA1_HUMAN | Q9UJY51j2j 1jwf 1jwg 1na8 1naf 1nwm 1o3x 1om9 1oxz 1py1 1ujj 1ujk 2dwx 2dwy 3g2s 3g2t 3g2u 3g2v 3g2w
        RABE1_HUMAN | Q152761p4u 1tu3 4n3y 4n3z 4q9u

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1X79)