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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PROLYL-TRNA SYNTHETASE (PRS) IN COMPLEX WITH INHIBITOR
 
Authors :  K. Okada, R. J. Skene
Date :  24 Mar 17  (Deposition) - 31 May 17  (Release) - 07 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.36
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminoacyl-Trna Synthetase, Atp Dependent, Inhibitor, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Adachi, K. Okada, R. Skene, K. Ogawa, M. Miwa, K. Tsuchinaga, S. Ohkubo, T. Henta, T. Kawamoto
Discovery Of A Novel Prolyl-Trna Synthetase Inhibitor And Elucidation Of Its Binding Mode To The Atp Site In Complex With L-Proline.
Biochem. Biophys. Res. V. 488 393 2017 Commun.
PubMed-ID: 28501621  |  Reference-DOI: 10.1016/J.BBRC.2017.05.064

(-) 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: UNP RESIDUES 998-1512
    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,GLUTAMATYL-PROLYL-TRNA SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
191Y2Ligand/Ion3-[(CYCLOHEXANECARBONYL)AMINO]-N-(2,3-DIHYDRO-1H-INDEN-2-YL)PYRAZINE-2-CARBOXAMIDE
2PRO2Mod. Amino AcidPROLINE
3ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:1152 , GLU A:1154 , HIS A:1157 , PHE A:1161 , LEU A:1162 , ARG A:1163 , THR A:1164 , PHE A:1167 , GLN A:1237 , THR A:1240 , THR A:1276 , ARG A:1278 , HOH A:1718binding site for residue 91Y A 1601
2AC2SOFTWARETHR A:1121 , GLU A:1123 , ARG A:1152 , TRP A:1169 , PHE A:1216 , HIS A:1242 , SER A:1272 , TRP A:1273 , GLY A:1274 , HOH A:1723binding site for residue PRO A 1602
3AC3SOFTWARECYS A:1448 , CYS A:1453 , CYS A:1495 , CYS A:1497binding site for residue ZN A 1603
4AC4SOFTWAREARG B:1152 , GLU B:1154 , LYS B:1156 , PHE B:1161 , LEU B:1162 , ARG B:1163 , THR B:1164 , PHE B:1167 , THR B:1240 , GLY B:1274 , THR B:1276 , ARG B:1278 , HOH B:1734binding site for residue 91Y B 1601
5AC5SOFTWARETHR B:1121 , GLU B:1123 , ARG B:1152 , GLU B:1171 , PHE B:1216 , HIS B:1242 , TRP B:1273 , GLY B:1274binding site for residue PRO B 1602
6AC6SOFTWARECYS B:1448 , CYS B:1453 , CYS B:1495 , CYS B:1497binding site for residue ZN B 1603

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:1453 -A:1497

(-) 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 5VAD)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VAD)

(-) 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:481
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhh..eee......eeehhhhhhhhhhhhhhhhhhhhhh..ee.....eehhhhhhhhhhhhhhhh...eeeeee..eeeeeeeee...hhhhhhhhhhhhh.hhhhh.eeeeeeeeee..............eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeee...........eeeeeeeee....eeeeeeeeeeeehhhhhhhh.eee.......eee.eeeeeeeehhhhhhhhhhhh.......hhhhh...eeeee....hhhhhhhhhhhhhhhhhhhhh....eee......hhhhhhhhhhhh...eeeeehhhhhhh.eeeeee.....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhheee..hhhhhhhhhhh..eeeeee..hhhhhhhhhhh.....eeeeee...................eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vad A 1016 LEAKKEENLADWYSQVITKSEMIEYHDISGCYILRPWAYAIWEAIKDFFDAEIKKLGVENCYFPMFVSQSALEKEKTHVADFAPEVAWVTRSGKTELAEPIAIRPTSETVMYPAYAKWVQSHRDLPIKLNQWCNVVRWEFKHPQPFLRTREFLWQEGHSAFATMEEAAEEVLQILDLYAQVYEELLAIPVVKGRKTEKEKFAGGDYTTTIEAFISASGRAIQGGTSHHLGQNFSKMFEIVFEDPKIPGEKQFAYQNSWGLTTRTIGVMTMVHGDNMGLVLPPRVACVQVVIIPCGILSEEDKEALIAKCNDYRRRLLSVNIRVRADLRDNYSPGWKFNHWELKGVPIRLEVGPRDMKSCQFVAVRRDTGEKLTVAENEAETKLQAILEDIQVTLFTRASEDLKTHMVVANTMEDFQKILDSGKIVQIPFCGEIDCEDWIKKTTAMGAKSLCIPFKPLCELQPGAKCVCNPAKYYTLFGRSY 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   || 1479      1489      1501      1511 
                                                                                                                                                                                                                                                                                                                                1311|                                                                                                                                               1462|                   1497|            
                                                                                                                                                                                                                                                                                                                                 1315                                                                                                                                                1474                    1500            


Chain B 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.hhhhhhhhhhhhhhhhhhhhhhh.....eeee...........eeeeeeeee....eeeeeeeeeeeehhhhhhh..ee.........ee.eeeeeeeehhhhhhhhhhhh...............eeeee....hhhhhhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhh...eeeeehhhhhhh.eeeeee.....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhheee..hhhhhhhhhh...eeeeee..hhhhhhhhhhhhh....eeeeee...................eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vad B 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
   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 5VAD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        SYEP_HUMAN | P07814: 1fyj 4hvc 4k86 4k87 4k88 5a1n 5a34 5a5h 5bmu

(-) Related Entries Specified in the PDB File

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