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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RALA-GPPNHP-SEC5 RAL-BINDING DOMAIN COMPLEX
 
Authors :  S. Fukai, H. T. Matern, R. H. Scheller, A. T. Brunger
Date :  09 Mar 03  (Deposition) - 15 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Small Gtp-Binding Protein, Immunogloblin-Like Fold, Beta- Sandwich, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Fukai, H. T. Matern, J. R. Jagath, R. H. Scheller, A. T. Brunger
Structural Basis Of The Interaction Between Rala And Sec5, A Subunit Of The Sec6/8 Complex
Embo J. V. 22 3267 2003
PubMed-ID: 12839989  |  Reference-DOI: 10.1093/EMBOJ/CDG329
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN RAL-A
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX2T
    Expression System StrainBL21-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 9-183
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRALA
 
Molecule 2 - EXOCYST COMPLEX COMPONENT SEC5
    ChainsC, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX2T
    Expression System StrainBL21-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DOMAIN, SEC5 RAL-BINDING DOMAIN
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymRSEC5

 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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GNP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:28 , THR A:46 , GNP A:200 , HOH A:348 , HOH A:352BINDING SITE FOR RESIDUE MG A 300
2AC2SOFTWARESER B:28 , THR B:46 , GNP B:1200 , HOH B:1255 , HOH B:1263BINDING SITE FOR RESIDUE MG B 300
3AC3SOFTWAREGLY A:23 , GLY A:24 , VAL A:25 , GLY A:26 , LYS A:27 , SER A:28 , ALA A:29 , PHE A:39 , VAL A:40 , GLU A:41 , ASP A:42 , PRO A:45 , THR A:46 , GLY A:71 , ASN A:127 , LYS A:128 , ASP A:130 , SER A:157 , ALA A:158 , MG A:300 , HOH A:332 , HOH A:335 , HOH A:348BINDING SITE FOR RESIDUE GNP A 200
4AC4SOFTWAREGLY B:23 , GLY B:24 , VAL B:25 , GLY B:26 , LYS B:27 , SER B:28 , ALA B:29 , PHE B:39 , VAL B:40 , GLU B:41 , ASP B:42 , TYR B:43 , PRO B:45 , THR B:46 , GLY B:71 , ASN B:127 , LYS B:128 , ASP B:130 , LEU B:131 , SER B:157 , ALA B:158 , MG B:300 , HOH B:1246 , HOH B:1255 , HOH B:1262 , HOH B:1263BINDING SITE FOR RESIDUE GNP B 1200

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser C:14 -Pro C:15
2Ser D:14 -Pro D:15

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UAD)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000000052571aENSE00001829077chr7:39663082-39663424343RALA_HUMAN-00--
1.3aENST000000052573aENSE00000832451chr7:39726230-39726380151RALA_HUMAN1-38382A:11-38
B:11-38
28
28
1.4bENST000000052574bENSE00000679279chr7:39729981-39730189209RALA_HUMAN39-108702A:39-108
B:39-108
70
70
1.5ENST000000052575ENSE00000679282chr7:39736284-39736458175RALA_HUMAN108-166592A:108-166
B:108-166
59
59
1.8dENST000000052578dENSE00001270055chr7:39745722-397477232002RALA_HUMAN167-206402A:167-183
B:167-183
17
17

(-) 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:173
 aligned with RALA_HUMAN | P11233 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:173
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180   
           RALA_HUMAN    11 SLALHKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQIDILDTAGQEDYAAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSVEEAKNRAEQWNVNYVETSAKTRANVDKVFFDLMREIRARKMEDS 183
               SCOP domains d1uada_ A: Ras-related protein RalA                                                                                                                                           SCOP domains
               CATH domains 1uadA00 A:11-183 P-loop containing nucleotide triphosphate hydrolases                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.....hhhhhhhhhhhh..........eeeeeeeeee..eeeeeeeeee......hhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhh..hhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: A:11-38     Exon 1.4b  PDB: A:39-108 UniProt: 39-108                              ----------------------------------------------------------Exon 1.8d         Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------Exon 1.5  PDB: A:108-166 UniProt: 108-166                  ----------------- Transcript 1 (2)
                 1uad A  11 SLALHKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQIDILDTAGQEDYAAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSVEEAKNRAEQWNVNYVETSAKTRANVDKVFFDLMREIRARKMEDS 183
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180   

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with RALA_HUMAN | P11233 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:173
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180   
           RALA_HUMAN    11 SLALHKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQIDILDTAGQEDYAAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSVEEAKNRAEQWNVNYVETSAKTRANVDKVFFDLMREIRARKMEDS 183
               SCOP domains d1uadb_ B: Ras-related protein RalA                                                                                                                                           SCOP domains
               CATH domains 1uadB00 B:11-183 P-loop containing nucleotide triphosphate hydrolases                                                                                                         CATH domains
           Pfam domains (1) -----Ras-1uadB01 B:16-177                                                                                                                                              ------ Pfam domains (1)
           Pfam domains (2) -----Ras-1uadB02 B:16-177                                                                                                                                              ------ Pfam domains (2)
         Sec.struct. author ...eeeeeee.....hhhhhhhhhhhh..........eeeeeeeeee..eeeeeeeeee......hhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeeehhhhhhhh..hhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: B:11-38     Exon 1.4b  PDB: B:39-108 UniProt: 39-108                              ----------------------------------------------------------Exon 1.8d         Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------Exon 1.5  PDB: B:108-166 UniProt: 108-166                  ----------------- Transcript 1 (2)
                 1uad B  11 SLALHKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQIDILDTAGQEDYAAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSVEEAKNRAEQWNVNYVETSAKTRANVDKVFFDLMREIRARKMEDS 183
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180   

Chain C from PDB  Type:PROTEIN  Length:92
 aligned with EXOC2_RAT | O54921 from UniProtKB/Swiss-Prot  Length:924

    Alignment length:92
                                    13        23        33        43        53        63        73        83        93  
            EXOC2_RAT     4 SRQPPLVTGISPNEGIPWTKVTIRGENLGTGPTDLIGLTICGHNCLLTAEWMSASKIVCRVGQAKNDKGDIIVTTKSGGRGTSTVSFKLLKP  95
               SCOP domains d1uadc_ C: Exocyst complex component Sec5, Ral-binding domain                                SCOP domains
               CATH domains 1uadC00 C:4-95 Immunoglobulins                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..ee....eeeeeee....hhh.eeeeee..ee.hhhheeee..eeeee..........eeeee...ee.ee....ee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 1uad C   4 SRQPPLVTGISPNEGIPWTKVTIRGENLGTGPTDLIGLTICGHNCLLTAEWMSASKIVCRVGQAKNDKGDIIVTTKSGGRGTSTVSFKLLKP  95
                                    13        23        33        43        53        63        73        83        93  

Chain D from PDB  Type:PROTEIN  Length:92
 aligned with EXOC2_RAT | O54921 from UniProtKB/Swiss-Prot  Length:924

    Alignment length:92
                                    13        23        33        43        53        63        73        83        93  
            EXOC2_RAT     4 SRQPPLVTGISPNEGIPWTKVTIRGENLGTGPTDLIGLTICGHNCLLTAEWMSASKIVCRVGQAKNDKGDIIVTTKSGGRGTSTVSFKLLKP  95
               SCOP domains d1uadd_ D: Exocyst complex component Sec5, Ral-binding domain                                SCOP domains
               CATH domains 1uadD00 D:4-95 Immunoglobulins                                                               CATH domains
           Pfam domains (1) ----TIG-1uadD01 D:8-92                                                                   --- Pfam domains (1)
           Pfam domains (2) ----TIG-1uadD02 D:8-92                                                                   --- Pfam domains (2)
         Sec.struct. author .....eeeeee..ee....eeeeeee....hhh.eeeeee..ee.hhhheeee..eeeee..........eeeee...ee.ee....ee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 1uad D   4 SRQPPLVTGISPNEGIPWTKVTIRGENLGTGPTDLIGLTICGHNCLLTAEWMSASKIVCRVGQAKNDKGDIIVTTKSGGRGTSTVSFKLLKP  95
                                    13        23        33        43        53        63        73        83        93  

   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, 4)

Asymmetric Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: E-set (290)
(-)
Family: Ras (176)
2aRas-1uadB01B:16-177
2bRas-1uadB02B:16-177

(-) Gene Ontology  (39, 41)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RALA_HUMAN | P11233)
molecular function
    GO:0051117    ATPase binding    Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
    GO:0031755    Edg-2 lysophosphatidic acid receptor binding    Interacting selectively and non-covalently with an Edg-2 lysophosphatidic acid receptor.
    GO:0019003    GDP binding    Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0017022    myosin binding    Interacting selectively and non-covalently with any part of a myosin complex; myosins are any of a superfamily of molecular motor proteins that bind to actin and use the energy of ATP hydrolysis to generate force and movement along actin filaments.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0007265    Ras protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
    GO:0031532    actin cytoskeleton reorganization    A process that is carried out at the cellular level which results in dynamic structural changes to the arrangement of constituent parts of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0000910    cytokinesis    The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells.
    GO:0006887    exocytosis    A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
    GO:0061024    membrane organization    A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
    GO:0051665    membrane raft localization    Any process in which membrane rafts are transported to, or maintained in, a specific location. Membrane rafts are small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes.
    GO:0001843    neural tube closure    The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
    GO:0051491    positive regulation of filopodium assembly    Any process that activates or increases the frequency, rate or extent of the assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone.
    GO:0017157    regulation of exocytosis    Any process that modulates the frequency, rate or extent of exocytosis.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0032154    cleavage furrow    The cleavage furrow is a plasma membrane invagination at the cell division site. The cleavage furrow begins as a shallow groove and eventually deepens to divide the cytoplasm.
    GO:0030659    cytoplasmic vesicle membrane    The lipid bilayer surrounding a cytoplasmic vesicle.
    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: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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030496    midbody    A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    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 C,D   (EXOC2_RAT | O54921)
molecular function
    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:0006893    Golgi to plasma membrane transport    The directed movement of substances from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane, where they fuse and release their contents by exocytosis.
    GO:0001927    exocyst assembly    The aggregation, arrangement and bonding together of various polypeptides into the exocyst complex.
    GO:0006887    exocytosis    A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
    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.
cellular component
    GO:0000145    exocyst    A protein complex peripherally associated with the plasma membrane that determines where vesicles dock and fuse. At least eight complex components are conserved between yeast and mammals.

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        RALA_HUMAN | P112331zc3 1zc4 2a78 2a9k 2bov

(-) Related Entries Specified in the PDB File

1c1y 1he8 1k8r 1lfd