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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN TRAP1 WITH AMPPNP
 
Authors :  C. Lee, H. K. Park, J. H. Ryu, B. H. Kang
Date :  27 Mar 15  (Deposition) - 29 Apr 15  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Mitochondrial Hsp90, Amppnp, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Lee, H. K. Park, H. Jeong, J. Lim, A. J. Lee, K. Y. Cheon, C. S. Kim, A. P. Thomas, B. Bae, N. D. Kim, S. H. Kim, P. G. Suh, J. H. Ryu, B. H. Kang
Development Of A Mitochondria-Targeted Hsp90 Inhibitor Base On The Crystal Structures Of Human Trap1
J. Am. Chem. Soc. V. 137 4358 2015
PubMed-ID: 25785725  |  Reference-DOI: 10.1021/JA511893N

(-) Compounds

Molecule 1 - HEAT SHOCK PROTEIN 75 KDA, MITOCHONDRIAL
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 60-561
    Gene: TRAP1, HSP75
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HSP 75,TNFR-ASSOCIATED PROTEIN 1,TUMOR NECROSIS FACTOR TYPE 1 RECEPTOR-ASSOCIATED PROTEIN,TRAP-1

 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, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1ANP4Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:115 , ASN A:119 , ALA A:123 , LYS A:126 , ASP A:158 , MET A:163 , ASN A:171 , SER A:178 , GLY A:179 , SER A:180 , GLY A:199 , GLN A:200 , PHE A:201 , GLY A:202 , VAL A:203 , GLY A:204 , PHE A:205 , THR A:251 , ARG A:402 , MG A:802binding site for residue ANP A 801
02AC2SOFTWAREASN A:119 , ANP A:801binding site for residue MG A 802
03AC3SOFTWAREASN B:119 , ANP B:801binding site for residue MG B 802
04AC4SOFTWAREASN C:119 , ANP C:801binding site for residue MG C 802
05AC5SOFTWAREASN D:119 , ANP D:801binding site for residue MG D 802
06AC6SOFTWAREGLU B:115 , LEU B:116 , ILE B:117 , SER B:118 , ALA B:120 , SER B:121 , ASP B:122 , ALA B:123 , ASP B:158 , MET B:163 , ASN B:171 , SER B:178 , GLY B:179 , SER B:180 , GLY B:199 , GLN B:200 , PHE B:201 , GLY B:202 , VAL B:203 , GLY B:204 , PHE B:205 , THR B:251 , ARG B:402 , MG B:802binding site for Di-peptide ANP B 801 and ASN B 119
07AC7SOFTWAREARG B:114 , GLU B:115 , ASN B:119 , ALA B:123 , ASP B:158 , MET B:163 , ASN B:171 , SER B:178 , GLY B:179 , SER B:180 , ILE B:198 , GLY B:199 , GLN B:200 , PHE B:201 , GLY B:202 , VAL B:203 , GLY B:204 , PHE B:205 , THR B:251 , ASN B:399 , LEU B:400 , SER B:401 , GLU B:403 , LEU B:404 , MG B:802binding site for Di-peptide ANP B 801 and ARG B 402
08AC8SOFTWAREGLU C:115 , LEU C:116 , ILE C:117 , SER C:118 , ALA C:120 , SER C:121 , ASP C:122 , ALA C:123 , LYS C:126 , ASP C:158 , MET C:163 , ASN C:171 , LEU C:172 , ARG C:177 , SER C:178 , GLY C:179 , SER C:180 , GLY C:199 , GLN C:200 , PHE C:201 , GLY C:202 , VAL C:203 , GLY C:204 , PHE C:205 , THR C:251 , ARG C:402 , MG C:802binding site for Di-peptide ANP C 801 and ASN C 119
09AC9SOFTWAREARG D:114 , GLU D:115 , ASN D:119 , ALA D:123 , LYS D:126 , ASP D:158 , MET D:163 , ASN D:171 , SER D:178 , GLY D:179 , SER D:180 , ILE D:198 , GLY D:199 , GLN D:200 , PHE D:201 , GLY D:202 , VAL D:203 , GLY D:204 , PHE D:205 , THR D:251 , ASN D:399 , LEU D:400 , SER D:401 , GLU D:403 , LEU D:404 , MG D:802binding site for Di-peptide ANP D 801 and ARG D 402
10AD1SOFTWAREGLU D:115 , LEU D:116 , ILE D:117 , SER D:118 , ALA D:120 , SER D:121 , ASP D:122 , ALA D:123 , LYS D:126 , ASP D:158 , MET D:163 , ASN D:171 , SER D:178 , GLY D:179 , SER D:180 , GLY D:199 , GLN D:200 , PHE D:201 , GLY D:202 , VAL D:203 , GLY D:204 , PHE D:205 , THR D:251 , ARG D:402 , MG D:802binding site for Di-peptide ANP D 801 and ASN D 119

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1B:501 -B:527
2C:501 -C:527
3D:501 -D:527

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Ala A:335 -Pro A:336
2Thr A:377 -Asp A:378
3Ala B:335 -Pro B:336
4Thr B:377 -Asp B:378
5Gln B:530 -Phe B:531
6Ala C:335 -Pro C:336
7Thr C:377 -Asp C:378
8Thr D:377 -Asp D:378
9Gln D:530 -Phe D:531

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z1I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z1I)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z1I)

(-) 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:365
                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeeee.eehhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee....eeeeee.....hhhhhhhhhhee..hhhhhhhh..hhhhh.......hhhhhhhh.eeeeeeeee.......eeeeee....eeeeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhhhh......eee..ee.....hhhhh.hhhhhhhhh.....eeeeeeeee.....eeeeeeee.......eeeee..eeeeeee....hhhhh..eeeee................hhhhhhhhhhhhhhhhhhhhhh..............hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z1i A  70 PLHSIISSTESVQGSTSKHEFQAETKKLLDIVARSLYSEKEVFIRELISNASDALEKLRHKLVSDGQALPEMEIHLQTNAEKGTITIQDTGIGMTQEELVSNLGTIARSGSKAFLDALAEASSKIIGQFGVGFYSAFMVADRVEVYSRSAAPGSLGYQWLSDGSGVFEIAEASGVRTGTKIIIHLKSDCKEFSSEARVRDVVTKYSNFVSFPLYLNGRRMNTLQAIWMMQHEEFYRYVAQAHDKPRYTLHYKTDAPLNIRSIFYVPDMKPSMSVALYSRKVLIQTKATDILPKWLRFIRGVVDSEDIPLNLSRELLQESALIRKLRDVLQQRLIKFFIDQSKKDAEKYAKFFEDYGLFMREGIVT 454
                                    79        89        99       109       119       129       139       149       159       169       179       192       202       212       222       232       242       252       262       272       282       292       310       320       330       340       350 ||    369       379       389       399       409       419       429       439       449     
                                                                                                                                               187|                                                                                                           301|                                       352|                                                                                            
                                                                                                                                                191                                                                                                            310                                        362                                                                                            


Chain B from PDB  Type:PROTEIN  Length:472
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee....eeee.eehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee....eeeeee.....hhhhhhhhhhee..hhhhhhhh..hhhhh.......hhhhhhh.eeeeeeeee.......eeeeee....eeeeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhhhh......eee..ee.....hhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeee...eeeeeeeee........eeeee..eeee.......hhhhh..eeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..eeee........eehhhhhhh......eeeeee..hhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhee..eeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z1i B  70 PLHSIISSTESVQGSTSKHEFQAETKKLLDIVARSLYSEKEVFIRELISNASDALEKLRHKLVSDGQALPEMEIHLQTNAEKGTITIQDTGIGMTQEELVSNLGTIARSGSKAFLDAAEASSKIIGQFGVGFYSAFMVADRVEVYSRSAAPGSLGYQWLSDGSGVFEIAEASGVRTGTKIIIHLKSDCKEFSSEARVRDVVTKYSNFVSFPLYLNGRRMNTLQAIWMMDPKDVREWQHEEFYRYVAQAHDKPRYTLHYKTDAPLNIRSIFYVPDMKPSMFSVALYSRKVLIQTKATDILPKWLRFIRGVVDSEDIPLNLSRELLQESALIRKLRDVLQQRLIKFFIDQSKKDAEKYAKFFEDYGLFMREGIVTATEQEVKEDIAKLLRYESSALPSGQLTSLSEYASRMRAGTRNIYYLCAPNRHLAEHSPYYEAMKKKDTEVLFCFEQFDELTLLHLREFDKKKLISVETD 553
                                    79        89        99       109       119       129       139       149       159       169       179      |193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353|      371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551  
                                                                                                                                              186|                                                                                                                                                               353|                                                                                                                                                                                               
                                                                                                                                               191                                                                                                                                                                362                                                                                                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:471
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee....eeee.eehhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee....eeeeee.....hhhhhhhhhhee..hhhhhhhh...hhhhh.......hhhhhhh.eeeeeeeee.......eeeeee....eeeeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhhhh......eee..ee.....hhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee.....eeeeeeee......eeeee..eeeeeee....hhhhh..eeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..eeee........eehhhhhhhh.........ee..hhhhhhhhhhhhhhhhh....eee...hhhhhhhhhhee..ee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z1i C  70 PLHSIISSTESVQGSTSKHEFQAETKKLLDIVARSLYSEKEVFIRELISNASDALEKLRHKLVSDGQALPEMEIHLQTNAEKGTITIQDTGIGMTQEELVSNLGTIARSGSKAFLDALAEASSKIIGQFGVGFYSAFMVADRVEVYSRSAAPGSLGYQWLSDGSGVFEIAEASGVRTGTKIIIHLKSDCKEFSSEARVRDVVTKYSNFVSFPLYLNGRRMNTLQAIWMMDPKDVREWQHEEFYRYVAQAHDKPRYTLHYKTDAPLNIRSIFYVPDMKPSSVALYSRKVLIQTKATDILPKWLRFIRGVVDSEDIPLNLSRELLQESALIRKLRDVLQQRLIKFFIDQSKKDAEKYAKFFEDYGLFMREGIVTATEQEVKEDIAKLLRYESSALPSGQLTSLSEYASRMRAGTRNIYYLCAPNRHLAEHSPYYEAMKKKDTEVLFCFEQFDELTLLHLREFDKKKLISVETD 553
                                    79        89        99       109       119       129       139       149       159       169       179       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552 
                                                                                                                                               187|                                                                                                                                                             351|                                                                                                                                                                                               
                                                                                                                                                191                                                                                                                                                              362                                                                                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:449
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeeee.eehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee....eeeeee.....hhhhhhhhhhee..hhhhhhhh.............hhhhhhh.eeeeeeeee.......eeeeee....eeeeeeee....eeeeeeee...hhhhhhhhhhhhhhhhhh......eee..ee.....hhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee.....eeeeeeee..............eeee..eeee.......hhhhh..eeeee................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..eeee......eee..hhhhhh...eeeee...eee...hhhhhhhhhhee..eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z1i D  70 PLHSIISSTESVQGSTSKHEFQAETKKLLDIVARSLYSEKEVFIRELISNASDALEKLRHKLVSDGQALPEMEIHLQTNAEKGTITIQDTGIGMTQEELVSNLGTIARSGSKAFLDAEASSKIIGQFGVGFYSAFMVADRVEVYSRSAAPGSLGYQWLSDGSGVFEIAEASGVRTGTKIIIHLKSDCKEFSSEARVRDVVTKYSNFVSFPLYLNGRRMNTLQAIWMMDPKDVREWQHEEFYRYVAQAHDKPRYTLHYKTDAPLNIRSIFYVPDMKPSMFDVSRSSVALYSRKVLIQTKATDILPKWLRFIRGVVDSEDIPLNLSRELLQESALIRKLRDVLQQRLIKFFIDQSKKDAEKYAKFFEDYGLFMREGIVTATEQEVKEDIAKLLRYESSALPSQLTSLSEYASRMTRNIYYLCAPVLFCFEQFDELTLLHLREFDKKKLISV 550
                                    79        89        99       109       119       129       139       149       159       169       179      |194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354  ||   367       377       387       397       407       417       427       437       447       457       467       477|      488 ||    501 ||    531       541         
                                                                                                                                              186|                                                                                                                                                                  357|                                                                                                                 477|        490|      503|                          
                                                                                                                                               192                                                                                                                                                                   361                                                                                                                  479         494       524
   Legend:   → Mismatch (orange background)
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  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 4Z1I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z1I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z1I)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)

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  4z1i
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  TRAP1_HUMAN | Q12931
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 Related Entries

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

UniProtKB/Swiss-Prot
        TRAP1_HUMAN | Q12931: 4z1f 4z1g 4z1h 5f3k 5f5r 5hph

(-) Related Entries Specified in the PDB File

4z1f 4z1g 4z1h