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(-) Description

Title :  HUMAN GIVD CYTOSOLIC PHOSPHOLIPASE A2
 
Authors :  H. Wang, M. G. Klein
Date :  24 Mar 16  (Deposition) - 08 Jun 16  (Release) - 22 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Signal Transduction, Phospholipase, Alpha/Beta Hydrolase, Calcium Binding, C2 Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Wang, M. G. Klein, G. Snell, W. Lane, H. Zou, I. Levin, K. Li, B. C. Sang
Structure Of Human Givd Cytosolic Phospholipase A2 Reveals Insights Into Substrate Recognition.
J. Mol. Biol. V. 428 2769 2016
PubMed-ID: 27220631  |  Reference-DOI: 10.1016/J.JMB.2016.05.012

(-) Compounds

Molecule 1 - CYTOSOLIC PHOSPHOLIPASE A2 DELTA
    Chains: B, A
    EC Number: 3.1.1.4
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 2-810
    Gene: PLA2G4D
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CPLA2-DELTA,PHOSPHOLIPASE A2 GROUP IVD

 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  (1, 14)

Asymmetric Unit (1, 14)
No.NameCountTypeFull Name
1SO414Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 2 (1, 10)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO B:662 , GLY B:663 , ARG B:665 , HOH B:1171binding site for residue SO4 B 901
02AC2SOFTWAREARG B:449binding site for residue SO4 B 902
03AC3SOFTWAREGLN B:600 , PRO B:641 , ARG B:642 , HOH B:1168 , HOH B:1216binding site for residue SO4 B 903
04AC4SOFTWAREASN B:470 , PHE B:621 , PRO B:633 , SER B:634 , GLN B:635 , HOH B:1014binding site for residue SO4 B 904
05AC5SOFTWAREARG A:596 , THR B:474 , LEU B:475 , ASP B:476binding site for residue SO4 B 905
06AC6SOFTWAREARG B:245 , THR B:248 , LYS B:251binding site for residue SO4 B 906
07AC7SOFTWAREARG B:415 , PRO B:518 , ARG B:519 , PHE B:522 , HOH B:1118binding site for residue SO4 B 907
08AC8SOFTWAREHIS B:281 , ASN B:285 , HOH B:1008binding site for residue SO4 B 908
09AC9SOFTWAREILE B:526 , ARG B:601 , SER B:602 , LEU B:643 , CYS B:644 , LEU B:645 , HOH B:1004binding site for residue SO4 B 909
10AD1SOFTWAREMET B:335 , TYR B:339 , TRP B:365 , THR B:366 , HIS B:369 , ALA B:388 , HOH B:1012 , HOH B:1153binding site for residue SO4 B 910
11AD2SOFTWAREGLN A:129 , SER A:395 , LYS A:396 , LEU A:397 , SER A:577 , THR A:772binding site for residue SO4 A 901
12AD3SOFTWAREPRO A:662 , GLY A:663 , ARG A:665binding site for residue SO4 A 902
13AD4SOFTWAREGLN A:50 , PRO A:55 , GLY A:56 , MET A:57 , LYS A:58binding site for residue SO4 A 903
14AD5SOFTWAREPHE A:737 , LYS A:738 , HIS A:740 , SER A:741 , ARG A:747 , GLU A:751 , LEU A:752 , GLY A:754 , GLY A:755binding site for residue SO4 A 904

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:163 -A:274

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala B:262 -Pro B:263
2Gln B:580 -Pro B:581

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IZ5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IZ5)

(-) Exons   (0, 0)

(no "Exon" information available for 5IZ5)

(-) 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:757
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.eeeeeeeeeeee.......eeeeeee......eee..........eeeeeeeeeee.....eeeeeeee.......eeeeeeeee.hhh.....eeeeee.......eeeeeeeeee.....eeeee...eee..eeeeeeee...eeeeee......eeeee.....eeeeeee....eeeeeeee.......eeeee......eeeeeeeee..eeeeeeeeeeee.......ee....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh..eeeee..hhhhhhhhhhhhhhhhhhh.hhhhh.eeee..hhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.....hhhhhhhhhh.....eeeeeeeee..........eeeeee....eee....eeehhhhh..eee..eeee.....hhhhhhhhhhhhhhhhhhhhhh.........................hhhhh..hhhhhhhh...................ee..hhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhh...hhhhhhh......eeeee.......hhhhhhhhhhhhhh.........hhhhhhh....eee.........eeeee....hhhh.eee..ee.hhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iz5 A  16 GEASTCWQLTVRVLEARNLRWAADPYVILQLSTAPGMKFKTKTLTDTSHPVWNEAFRFLIQSQVKNVLELSIYDEDSVTEDDICFKVLYDISEVLPGKLLRKTFSQSPQGEEELDVEFLMEETSDRPENLITNKVIVARELSCLDVHLDKLELELVLKGSYEDTQTSFLGTASAFRFHYMAALETELSGRLRSSNSAGYLTVPLRPLTIGKEVTMDVPAPNAPGVRLQLKAEGCPEELAVHLGFNLCAEEQAFLSRRKQVVAKALKQALQLDRDLQEDEVPVVGIMATGGGARAMTSLYGHLLALQKLGLLDCVTYFSGISGSTWTMAHLYGDPEWSQRDLEGPIRYAREHLAKSKLEVFSPERLASYRRELELRAEQGHPTTFVDLWALVLESMLHGQVMDQKLSGQRAALERGQNPLPLYLSLNVKENNLETLDFKEWVEFSPYEVGFLKYGAFVPPELFGSEFFMGRLMRRIPEPRICFLEAIWSNIFSLNLLDAWYDLTSSGESWKQHEPLTTSGTSSRLEASWLQPGTALAQAFKGFLTGRPLHQRSPNFLQGLQLHQDYCSHKDFSTWADYQLDSMPSQLTPKEPRLCLVDAAYFINTSSPSMFRPGRRLDLILSFDYSLSAPFEALQQTELYCRARGLPFPRVEPSPQDQHQPRECHLFSDPACPEAPILLHFPLVNASFKDHSAPGVQRSPAELQGGQVDLTGATCPYTLSNMTYKEEDFERLLRLSDYNVQTSQGAILQALRTALKHR 807
                                    25        35 ||     50        60        70        80        90       100       110       120       130       140       150       160       182       192       202       212       222   ||  240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550 ||    570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       
                                                37|                                                                                                                           169|                                         226|                                                                                                                                                                                                                                                                                                                          552|                                                                                                                                                                                                                                                    
                                                 43                                                                                                                            182                                          235                                                                                                                                                                                                                                                                                                                           563                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:746
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.eeeeeeeeeeee............eeeeeee.......ee..........eeeeeeeeeee.....eeeeeeee.......eeeeeeeee.hhh.....eeeee........eeeeeeeeee.....eeeee...eee..eeeeeee....eeeeeee......eeeee.....eeeeeee....eeeeeeeee..............eeeee......eeeeeee.......eeeeeeeee.......ee....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh..eeeee..hhhhhhhhhhhhhhhhhhh.hhhhh.eeee..hhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh......hhhhhhhhhh.....eeeeeeee............eeeee....eee....eeehhhhh..eee..eeee.....hhhhhhhhhh.......hhhhh.......hhhhhhhhh..................ee.hhhhhhhhhh.....ee...............eehhhhh...hhhhhhh......eeeee.......hhhhhhhhhhhhhh.........hhhhhhh....eee.........eeeee.........eee..ee.....hhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iz5 B  16 GEASTCWQLTVRVLEARNLRWADLLSEADPYVILQLSTAPGMKFKTKTLTDTSHPVWNEAFRFLIQSQVKNVLELSIYDEDSVTEDDICFKVLYDISEVLPGKLLRKTFSQSPQGEEELDVEFLMEETSDRPENLITNKVIVARELSCLDVHLDDKLELELVLKGSYEDTQTSFLGTASAFRFHYMAALETELSGRLRSSRSNGWNGDNSAGYLTVPLRPLTIGKEVTMDVPAPNAPGVRLQLKAEGCPEELAVHLGFNLCAEEQAFLSRRKQVVAKALKQALQLDRDLQEDEVPVVGIMATGGGARAMTSLYGHLLALQKLGLLDCVTYFSGISGSTWTMAHLYGDPEWSQRDLEGPIRYAREHLAKSKLEVFSPERLASYRRELELRAEQGHPTTFVDLWALVLESMLHGQVMDQKLSGQRAALERGQNPLPLYLSLNVKENNLETLDFKEWVEFSPYEVGFLKYGAFVPPELFGSEFFMGRLMRRIPEPRICFLEAIWSNIFSLNLLDAWYDSWLQPGTALAQAFKGFLTGRPLHQRSPNFLQGLQLHQDYCSHKDFSTWADYQLDSMPSQLTPKEPRLCLVDAAYFINTSSPSMFRPGRRLDLILSFDYSLSAPFEALQQTELYCRARGLPFPRVEPSPQDQHQPRECHLFSDPACPEAPILLHFPLVNASFKDHSAPGVQRSPAELQGGQVDLTGATCPYTLSNMTYKEEDFERLLRLSDYNVQTSQGAILQALRTALKHR 807
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165   ||  186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536    || 581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801      
                                                                                                                                                                                   169|                                                                                                                                                                                                                                                                                                                                                                     541|                                                                                                                                                                                                                                      
                                                                                                                                                                                    181                                                                                                                                                                                                                                                                                                                                                                      577
   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 5IZ5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IZ5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IZ5)

(-) Gene Ontology  (22, 22)

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        PA24D_HUMAN | Q86XP0: 5ixc 5izr

(-) Related Entries Specified in the PDB File

5ixc