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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN GRP78 (70KDA HEAT SHOCK PROTEIN 5 / BIP) ATPASE DOMAIN IN COMPLEX WITH AMP-PCP
 
Authors :  S. J. Hughes, T. Antoshchenko, J. H. Song, J. Pizarro, H. W. Park
Date :  02 Dec 15  (Deposition) - 15 Jun 16  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Chaperone, Atpase Domain, Nucleotide-Binding, Endoplasmic Reticulum (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Hughes, T. Antoshchenko, Y. Chen, H. Lu, J. C. Pizarro, H. W. Park
Probing The Atp Site Of Grp78 With Nucleotide Triphosphate Analogs.
Plos One V. 11 54862 2016
PubMed-ID: 27144892  |  Reference-DOI: 10.1371/JOURNAL.PONE.0154862

(-) Compounds

Molecule 1 - 78 KDA GLUCOSE-REGULATED PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ATPASE DOMAIN (UNP RESIDUES 26-407)
    Gene: HSPA5, GRP78
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GRP-78, ENDOPLASMIC RETICULUM LUMENAL CA(2+)-BINDING PROTEIN GRP78, HEAT SHOCK 70 KDA PROTEIN 5, IMMUNOGLOBULIN HEAVY CHAIN- BINDING PROTEIN, BIP

 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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ACP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:36 , THR A:37 , THR A:38 , TYR A:39 , LYS A:96 , GLU A:201 , ASP A:224 , GLY A:226 , GLY A:227 , THR A:229 , GLY A:255 , GLU A:293 , LYS A:296 , ARG A:297 , SER A:300 , GLY A:363 , GLY A:364 , SER A:365 , ARG A:367 , ILE A:368 , MG A:502 , HOH A:601 , HOH A:602 , HOH A:609 , HOH A:618 , HOH A:625 , HOH A:642 , HOH A:663 , HOH A:674 , HOH A:688binding site for residue ACP A 501
2AC2SOFTWAREACP A:501 , HOH A:618 , HOH A:625 , HOH A:642 , HOH A:663binding site for residue MG A 502
3AC3SOFTWAREGLY B:36 , THR B:37 , THR B:38 , TYR B:39 , LYS B:96 , GLU B:201 , ASP B:224 , GLY B:226 , GLY B:227 , THR B:229 , GLY B:255 , GLU B:293 , LYS B:296 , ARG B:297 , SER B:300 , GLY B:363 , GLY B:364 , SER B:365 , ARG B:367 , ILE B:368 , MG B:502 , HOH B:602 , HOH B:603 , HOH B:604 , HOH B:607 , HOH B:616 , HOH B:625 , HOH B:627 , HOH B:640 , HOH B:644binding site for residue ACP B 501
4AC4SOFTWAREACP B:501 , HOH B:604 , HOH B:607 , HOH B:616 , HOH B:625binding site for residue MG B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F2R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5F2R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F2R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F2R)

(-) Exons   (0, 0)

(no "Exon" information available for 5F2R)

(-) 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:381
                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....eeeeeeee..eeee.........ee.eeee.....eeehhhhhh....hhhhhee.hhhh......hhhhhhhh.....eeeee..eeeeeee.....eeeehhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhh..eeeeeeehhhhhhhhh........eeeeeeee....eeeeeeeee..eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeehhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f2r A  27 VGTVVGIDLGTTYSCVGVFKNGRVEIIANDQGNRITPSYVAFTPEGERLIGDAAKNQLTSNPENTVFDAKRLIGRTWNDPSVQQDIKFLPFKVVEKKTKPYIQVDIGGGQTKTFAPEEISAMVLTKMKETAEAYLGKKVTHAVVTVPAYFNDAQRQATKDAGTIAGLNVMRIINEPTAAAIAYGLDKREGEKNILVFDLGGGTFDVSLLTIDNGVFEVVATNGDTHLGGEDFDQRVMEHFIKLYKKKTGKDVRKDNRAVQKLRREVEKAKRALSSQHQARIEIESFYEGEDFSETLTRAKFEELNMDLFRSTMKPVQKVLEDSDLKKSDIDEIVLVGGSTRIPKIQQLVKEFFNGKEPSRGINPDEAVAYGAAVQAGVLSG 407
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406 


Chain B from PDB  Type:PROTEIN  Length:379
                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....eeeeeeee..eeee.........ee.eeee.....eeehhhhhh...hhh.eee.hhhh......hhhhhhhhhhh..eeeee..eeeeeeeee..eeeeehhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhh..eeeeeeehhhhhhhhh........eeeeeeee....eeeeeeeee..eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeehhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f2r B  27 VGTVVGIDLGTTYSCVGVFKNGRVEIIANDQGNRITPSYVAFTPEGERLIGDAAKNQTSNPENTVFDAKRLIGRTWNDPSVQQDIKFLPFKVVEKKTKPYIQVDIGGGQTKTFAPEEISAMVLTKMKETAEAYLGKKVTHAVVTVPAYFNDAQRQATKDAGTIAGLNVMRIINEPTAAAIAYGLDKREGEKNILVFDLGGGTFDVSLLTIDNGVFEVVATNGDTHLGGEDFDQRVMEHFIKLYKKKTGKDVRKDNRAVQKLRREVEKAKRALSSQHQARIEIESFYEGEDFSETLTRAKFEELNMDLFRSTMKPVQKVLEDSDLKKSDIDEIVLVGGSTRIPKIQQLVKEFFNGKEPSRGINPDEAVAYGAAVQAGVLS 406
                                    36        46        56        66        76      ||87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397         
                                                                                   83|                                                                                                                                                                                                                                                                                                                                 
                                                                                    85
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  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 5F2R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F2R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F2R)

(-) Gene Ontology  (60, 60)

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  5f2r
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  GRP78_HUMAN | P11021
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 Related Entries

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

UniProtKB/Swiss-Prot
        GRP78_HUMAN | P11021: 3iuc 3ldl 3ldn 3ldo 3ldp 5e84 5e85 5e86 5evz 5ex5 5exw 5ey4 5f0x 5f1x

(-) Related Entries Specified in the PDB File

5evz 5ex5 5exw 5ey4 5f0x 5f1x