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(-) Description

Title :  IN MESO X-RAY CRYSTALLOGRAPHY STRUCTURE OF THE PEPTST-ALA-PHE COMPLEX AT 100 K
 
Authors :  C. -Y. Huang, V. Olieric, M. Wang, M. Caffrey
Date :  10 Aug 15  (Deposition) - 13 Jan 16  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Y. Huang, V. Olieric, P. Ma, N. Howe, L. Vogeley, X. Liu, R. Warshamanage, T. Weinert, E. Panepucci, B. Kobilka, K. Diederichs M. Wang, M. Caffrey
In Meso In Situ Serial X-Ray Crystallography Of Soluble And Membrane Proteins At Cryogenic Temperatures.
Acta Crystallogr D Struct V. 72 93 2016 Biol
PubMed-ID: 26894538  |  Reference-DOI: 10.1107/S2059798315021683

(-) Compounds

Molecule 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DTPT, STU0970
    Organism Scientific: STREPTOCOCCUS THERMOPHILUS (STRAIN ATCC BAA-250 / LMG 18311)
    Organism Taxid: 264199
    Synonym: PEPTST

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 26)

Asymmetric/Biological Unit (5, 26)
No.NameCountTypeFull Name
178M21Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
2ALA1Mod. Amino AcidALANINE
3PE52Ligand/Ion3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
4PHE1Mod. Amino AcidPHENYLALANINE
5PO41Ligand/IonPHOSPHATE ION

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:156 , GLU A:299 , ASN A:328 , GLU A:400 , PHE A:502binding site for residue ALA A 501
02AC2SOFTWAREARG A:26 , TYR A:30 , TYR A:68 , LYS A:126 , ILE A:155 , TRP A:427 , ALA A:501binding site for residue PHE A 502
03AC3SOFTWAREMET A:238 , TRP A:243 , ALA A:248 , ASN A:251binding site for residue 78M A 503
04AC4SOFTWARELEU A:212 , PRO A:214 , LEU A:221 , ALA A:376 , 78M A:505 , 78M A:506binding site for residue 78M A 504
05AC5SOFTWARELEU A:369 , LEU A:370 , ALA A:376 , VAL A:451 , 78M A:504 , 78M A:519binding site for residue 78M A 505
06AC6SOFTWARELEU A:212 , LEU A:220 , VAL A:224 , 78M A:504 , 78M A:523binding site for residue 78M A 506
07AC7SOFTWAREMET A:96 , ALA A:173 , VAL A:177 , PHE A:195 , 78M A:522 , PE5 A:525 , HOH A:601binding site for residue 78M A 507
08AC8SOFTWARESER A:385 , LEU A:387 , TRP A:388 , GLY A:391 , LEU A:395 , 78M A:512 , HOH A:649 , HOH A:663binding site for residue 78M A 508
09AC9SOFTWARELEU A:444 , TYR A:453 , PHE A:457binding site for residue 78M A 509
10AD1SOFTWAREVAL A:101 , PHE A:106 , ILE A:120 , VAL A:469 , PHE A:470 , 78M A:519 , 78M A:523binding site for residue 78M A 510
11AD2SOFTWARETRP A:318 , PHE A:319 , PRO A:386binding site for residue 78M A 511
12AD3SOFTWARELYS A:218 , VAL A:222 , SER A:225 , ILE A:232 , TYR A:378 , TRP A:388 , 78M A:508 , 78M A:518binding site for residue 78M A 512
13AD4SOFTWAREARG A:85 , PRO A:86 , PHE A:89 , TRP A:90 , LEU A:97 , TYR A:194 , 78M A:522 , HOH A:611binding site for residue 78M A 513
14AD5SOFTWAREILE A:115 , ILE A:116 , LEU A:246 , LEU A:253 , 78M A:515binding site for residue 78M A 514
15AD6SOFTWARETHR A:72 , ILE A:73 , ILE A:119 , ILE A:260 , 78M A:514binding site for residue 78M A 515
16AD7SOFTWAREASP A:48 , PHE A:106 , GLY A:107 , ALA A:108 , SER A:109binding site for residue PO4 A 516
17AD8SOFTWAREPHE A:289 , LEU A:437 , GLN A:440 , THR A:443 , 78M A:520binding site for residue 78M A 517
18AD9SOFTWAREVAL A:222 , LEU A:226 , 78M A:512binding site for residue 78M A 518
19AE1SOFTWARESER A:455 , TYR A:456 , LEU A:459 , ILE A:466 , 78M A:505 , 78M A:510binding site for residue 78M A 519
20AE2SOFTWAREILE A:255 , ILE A:258 , VAL A:262 , PHE A:263 , TRP A:267 , GLN A:440 , 78M A:517binding site for residue 78M A 520
21AE3SOFTWAREPHE A:231 , ILE A:235 , TYR A:249binding site for residue 78M A 521
22AE4SOFTWAREMET A:96 , PHE A:187 , TYR A:194 , 78M A:507 , 78M A:513binding site for residue 78M A 522
23AE5SOFTWARETHR A:72 , ILE A:73 , PHE A:76 , 78M A:506 , 78M A:510binding site for residue 78M A 523
24AE6SOFTWAREPHE A:9 , SER A:149 , ILE A:150 , PHE A:153 , LEU A:157 , TRP A:323binding site for residue 78M A 524
25AE7SOFTWAREGLY A:174 , TYR A:175 , HIS A:176 , 78M A:507binding site for residue PE5 A 525
26AE8SOFTWARETYR A:38 , TRP A:41 , PHE A:42 , SER A:45 , ARG A:53 , GLN A:170 , TYR A:175 , HOH A:655binding site for residue PE5 A 526

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D59)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5D59)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D59)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D59)

(-) Exons   (0, 0)

(no "Exon" information available for 5D59)

(-) 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:450
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5d59 A   5 GKTFFGQPLGLSTLFMTEMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAIYASMVYLSGTIGGFVADRIIGARPAVFWGGVLIMLGHIVLALPFGASALFGSIILIIIGTGFLKPNVSTLVGTLYDEHDRRRDAGFSIFVFGINLGAFIAPLIVGAAQEAAGYHVAFSLAAIGMFIGLLVYYFGGKKTLDPHYLRPTDPLAPEEVKPLLVKVSLAVAGFIAIIVVMNLVGWNSLPAYINLLTIVAIAIPVFYFAWMITSTEHLRVVSYIPLFIAAVLFWAIEEQGSVVLATFAAERVDSSWFPVSWFQSLNPLFIMLYTPFFAWLWTAWKKNQPSSPTKFAVGLMFAGLSFLLMAIPGALYGTSGKVSPLWLVGSWALVILGEMLISMMSMWFLSSSVGSALNAQLVTLYNAKSEVAYFSYFGLGSVVLGIVLVFLSKRIAF 502
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264    || 279       289       299       309       319       329       339       349       359       369       379       389       399    || 427       437       447       457       467       502
                                                                                                                                                                                                                                                                                                  269|                                                                                                                              404|                                                 475| 
                                                                                                                                                                                                                                                                                                   275                                                                                                                               423                                                  501
   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 5D59)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D59)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D59)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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        Q5M4H8_STRT2 | Q5M4H8: 4aps 4d2b 4d2c 4d2d 4xni 4xnj 5d58 5d6k 5mmt

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