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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PROLYL-TRNA SYNTHETASE IN COMPLEX WITH HALOFUGINONE AND ATP ANALOGUE
 
Authors :  H. Zhou, L. Sun, X. L. Yang, P. Schimmel
Date :  06 Nov 12  (Deposition) - 02 Jan 13  (Release) - 13 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Zhou, L. Sun, X. L. Yang, P. Schimmel
Atp-Directed Capture Of Bioactive Herbal-Based Medicine On Human Trna Synthetase.
Nature V. 494 121 2012
PubMed-ID: 23263184  |  Reference-DOI: 10.1038/NATURE11774

(-) Compounds

Molecule 1 - BIFUNCTIONAL GLUTAMATE/PROLINE--TRNA LIGASE
    Chains: A, B
    EC Number: 6.1.1.17, 6.1.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: PRORS PART OF EPRS (UNP RESIDUES 1003-1513)
    Gene: EPRS, GLNS, PARS, QARS, QPRS, PIG32
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BIFUNCTIONAL AMINOACYL-TRNA SYNTHETASE, CELL PROLIFERATION- INDUCING GENE 32 PROTEIN, GLUTAMATE--TRNA LIGASE, GLUTAMYL-TRNA SYNTHETASE, GLURS, PROLINE--TRNA LIGASE, PROLYL-TRNA SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2HFG2Ligand/Ion7-BROMO-6-CHLORO-3-{3-[(2R,3S)-3-HYDROXYPIPERIDIN-2-YL]-2-OXOPROPYL}QUINAZOLIN-4(3H)-ONE
3MG2Ligand/IonMAGNESIUM ION
4ZN2Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:1152 , GLU A:1154 , PHE A:1161 , ARG A:1163 , THR A:1164 , PHE A:1167 , GLN A:1237 , GLY A:1239 , THR A:1240 , THR A:1276 , ARG A:1278 , HFG A:1602 , MG A:1603 , HOH A:1736 , HOH A:1780 , HOH A:1793BINDING SITE FOR RESIDUE ANP A 1601
2AC2SOFTWAREHIS A:1093 , PHE A:1097 , GLU A:1100 , VAL A:1101 , PRO A:1120 , THR A:1121 , GLU A:1123 , ARG A:1152 , TRP A:1169 , GLU A:1171 , HIS A:1173 , PHE A:1216 , HIS A:1242 , TRP A:1273 , GLY A:1274 , ANP A:1601 , HOH A:1794 , HOH A:1805BINDING SITE FOR RESIDUE HFG A 1602
3AC3SOFTWAREANP A:1601 , HOH A:1793 , HOH A:1794 , HOH A:1795BINDING SITE FOR RESIDUE MG A 1603
4AC4SOFTWARECYS A:1448 , CYS A:1453 , CYS A:1495 , CYS A:1497BINDING SITE FOR RESIDUE ZN A 1604
5AC5SOFTWAREARG B:1152 , GLU B:1154 , PHE B:1161 , LEU B:1162 , ARG B:1163 , THR B:1164 , PHE B:1167 , TRP B:1169 , GLN B:1237 , THR B:1240 , THR B:1276 , ARG B:1278 , HFG B:1602 , MG B:1603 , HOH B:1702 , HOH B:1706 , HOH B:1719 , HOH B:1725 , HOH B:1743 , HOH B:1752 , HOH B:1778 , HOH B:1784BINDING SITE FOR RESIDUE ANP B 1601
6AC6SOFTWAREHIS B:1093 , PHE B:1097 , GLU B:1100 , VAL B:1101 , PRO B:1120 , THR B:1121 , GLU B:1123 , ARG B:1152 , TRP B:1169 , PHE B:1216 , HIS B:1242 , TRP B:1273 , GLY B:1274 , ANP B:1601 , HOH B:1706 , HOH B:1766BINDING SITE FOR RESIDUE HFG B 1602
7AC7SOFTWAREANP B:1601 , HOH B:1706 , HOH B:1719 , HOH B:1778 , HOH B:1784BINDING SITE FOR RESIDUE MG B 1603
8AC8SOFTWARECYS B:1448 , CYS B:1453 , CYS B:1495 , CYS B:1497BINDING SITE FOR RESIDUE ZN B 1604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HVC)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:1140 -Pro A:1141
2Leu B:1140 -Pro B:1141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HVC)

(-) 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:482
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhh..eee......eeehhhhhhhhhhhhhhhhhhhhhh..ee.....eeehhhhh.....hhhhhhh.eeeeee..eeeeeeeee...hhhhhhhhhhhhh.hhhhh.eeeeeeeeee..............eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh......eeee...........eeeeeeeee....eeeeeeeeeeeehhhhhhhh.eee.......eee.eeeeeeeehhhhhhhhhhhh...............eeeee....hhhhhhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhh...eeeeehhhhhhhheeeeee.....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhheee..hhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhh...eeeeee...................eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4hvc A 1016 LEAKKEENLADWYSQVITKSEMIEYHDISGCYILRPWAYAIWEAIKDFFDAEIKKLGVENCYFPMFVSQSALEKEKTHVADFAPEVAWVTRSGKTELAEPIAIRPTSETVMYPAYAKWVQSHRDLPIKLNQWCNVVRWEFKHPQPFLRTREFLWQEGHSAFATMEEAAEEVLQILDLYAQVYEELLAIPVVKGRKTEKEKFAGGDYTTTIEAFISASGRAIQGGTSHHLGQNFSKMFEIVFEDPKIPGEKQFAYQNSWGLTTRTIGVMTMVHGDNMGLVLPPRVACVQVVIIPCGILSEEDKEALIAKCNDYRRRLLSVNIRVRADLRDNYSPGWKFNHWELKGVPIRLEVGPRDMKSCQFVAVRRDTGEKLTVAENEAETKLQAILEDIQVTLFTRASEDLKTHMVVANTMEDFQKILDSGKIVQIPFCGEIDCEDWIKKTTARMGAKSLCIPFKPLCELQPGAKCVCNPAKYYTLFGRSY 1512
                                  1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165      1175      1185      1195      1205      1215      1225      1235      1245      1255      1265      1275      1285      1295      1305     |1318      1328      1338      1348      1358      1368      1378      1388      1398      1408      1418      1428      1438      1448      1458    ||1478      1488      1500      1510  
                                                                                                                                                                                                                                                                                                                                1311|                                                                                                                                                1463|                   1497|            
                                                                                                                                                                                                                                                                                                                                 1315                                                                                                                                                 1474                    1500            


Chain B from PDB  Type:PROTEIN  Length:483
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhh..eee......eeehhhhhhhhhhhhhhhhhhhhhh..ee.....eeehhhhhh....hhhhhhh.eeeeee..eeeeeeeee...hhhhhhhhhhhhh.hhhhh.eeeeeeeeee..............eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeee...........eeeeeeeee....eeeeeeeeeeeehhhhhhhh.eee.......eee.eeeeeeeehhhhhhhhhhhh.......hhhhh...eeeee....hhhhhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhh...eeeeehhhhhhh.eeeeee.....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhheee..hhhhhhhhhh...eeeeee..hhhhhhhhhhhhh...eeeeee.....................eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4hvc B 1015 GLEAKKEENLADWYSQVITKSEMIEYHDISGCYILRPWAYAIWEAIKDFFDAEIKKLGVENCYFPMFVSQSALEKEKTHVADFAPEVAWVTRSGKTELAEPIAIRPTSETVMYPAYAKWVQSHRDLPIKLNQWCNVVRWEFKHPQPFLRTREFLWQEGHSAFATMEEAAEEVLQILDLYAQVYEELLAIPVVKGRKTEKEKFAGGDYTTTIEAFISASGRAIQGGTSHHLGQNFSKMFEIVFEDPKIPGEKQFAYQNSWGLTTRTIGVMTMVHGDNMGLVLPPRVACVQVVIIPCGISEEDKEALIAKCNDYRRRLLSVNIRVRADLRDNYSPGWKFNHWELKGVPIRLEVGPRDMKSCQFVAVRRDTGEKLTVAENEAETKLQAILEDIQVTLFTRASEDLKTHMVVANTMEDFQKILDSGKIVQIPFCGEIDCEDWIKKTTAMGAKSLCIPFKPLCELQPGAKCVCGKNPAKYYTLFGRSY 1512
                                  1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224      1234      1244      1254      1264      1274      1284      1294      1304      1318      1328      1338      1348      1358      1368      1378      1388      1398      1408      1418      1428      1438      1448      1458   || 1479      1489      1499      1509   
                                                                                                                                                                                                                                                                                                                                 1311|                                                                                                                                              1462|                                      
                                                                                                                                                                                                                                                                                                                                  1316                                                                                                                                               1474
   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  (0, 0)

(no "SCOP Domain" information available for 4HVC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)

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  4hvc
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        SYEP_HUMAN | P07814: 1fyj 4k86 4k87 4k88 5a1n 5a34 5a5h 5bmu 5vad

(-) Related Entries Specified in the PDB File

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