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(-) Description

Title :  STRUCTURAL INSIGHTS INTO THE DUAL STRATEGY OF RECOGNITION OF PEPTIDOGLYCAN RECOGNITION PROTEIN, PGRP-S: TERNARY COMPLEX OF PGRP-S WITH LPS AND FATTY ACID
 
Authors :  P. Sharma, D. Dube, M. Sinha, S. Yadav, P. Kaur, S. Sharma, T. P. Singh
Date :  03 Aug 12  (Deposition) - 26 Sep 12  (Release) - 15 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Peptidoglycan Binding, Immune Response, Secreted, Antimicrobial, Pgrp, Antibiotic, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Sharma, D. Dube, M. Sinha, S. Yadav, P. Kaur, S. Sharma, T. P. Singh
Structural Insights Into The Dual Strategy Of Recognition B Peptidoglycan Recognition Protein, Pgrp-S: Structure Of The Ternary Complex Of Pgrp-S With Lipopolysaccharide And Stearic Acid.
Plos One V. 8 53756 2013
PubMed-ID: 23326499  |  Reference-DOI: 10.1371/JOURNAL.PONE.0053756

(-) Compounds

Molecule 1 - PEPTIDOGLYCAN RECOGNITION PROTEIN 1
    Chains: A, B, C, D
    Organism Common: CAMEL,DROMEDARIES,DROMEDARY,ONE-HUMPED CAMEL
    Organism Scientific: CAMELUS DROMEDARIUS
    Organism Taxid: 9838
    Strain: CAMELUS DROMEDARIUS
    Synonym: PEPTIDOGLYCAN RECOGNITION PROTEIN SHORT, PGRP-S

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2LP51Ligand/Ion(R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE
3STE1Ligand/IonSTEARIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:126 , ALA A:129 , PRO B:4 , ALA B:5 , CYS B:6 , ARG D:31 , ARG D:138BINDING SITE FOR RESIDUE STE B 201
2AC2SOFTWAREASN A:140 , LEU C:64 , ALA C:92 , HIS C:93 , ALA C:94 , GLY C:95 , PRO C:96 , ASN C:99 , GLN C:150 , PRO C:151 , HOH C:627 , ALA D:94 , GLY D:95 , PRO D:96 , THR D:97 , TRP D:98 , ASN D:99 , LYS D:144 , VAL D:149 , GLN D:150 , PRO D:151BINDING SITE FOR RESIDUE LP5 C 501
3AC3SOFTWAREPRO C:151 , THR C:152 , HIS D:37 , ALA D:39 , TYR D:71 , HIS D:146BINDING SITE FOR RESIDUE GOL D 201

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1A:6 -A:130
2A:22 -A:67
3A:43 -A:49
4B:6 -B:130
5B:22 -B:67
6B:43 -B:49
7C:6 -C:130
8C:22 -C:67
9C:43 -C:49
10D:6 -D:130
11D:22 -D:67
12D:43 -D:49

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Ala A:5 -Cys A:6
2Arg A:28 -Pro A:29
3Ser A:154 -Pro A:155
4Ala B:5 -Cys B:6
5Arg B:28 -Pro B:29
6Ser B:154 -Pro B:155
7Pro C:4 -Ala C:5
8Arg C:28 -Pro C:29
9Ser C:154 -Pro C:155
10Pro D:4 -Ala D:5
11Arg D:28 -Pro D:29
12Ser D:154 -Pro D:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GF9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GF9)

(-) Exons   (0, 0)

(no "Exon" information available for 4GF9)

(-) 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:171
                                                                                                                                                                                                           
               SCOP domains d4gf9a_ A: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee...................eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee..........hhhhhh..eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeee.hhh......hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gf9 A   1 EDPPACGSIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQTWSHYRA 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 


Chain B from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains d4gf9b_ B: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eehhhhhh.............eeeeeeee.........hhhhhhhhhhhhhhhhh.........eee.....eee..........hhhhhh...eeeee.........hhhhhhhhhhhhhhhhh...eeeeeeeeehhhhh.....hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gf9 B   1 EDPPACGSIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQTWSHYRA 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 


Chain C from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains d4gf9c_ C: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eehhhhh..............eeeeeeee.......hhhhhhhhhhhhhhhhhh..........eee.....eee..............hhh.eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeeehhhhh.....hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gf9 C   1 EDPPACGSIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQTWSHYRA 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 


Chain D from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains d4gf9d_ D: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eehhhhhh.............eeeeeeee.......hhhhhhhhhhhhhhhhhh..........eee.....eee..........hhhhhh..eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeeehhhhh.....hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gf9 D   1 EDPPACGSIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQTWSHYRA 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GF9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GF9)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:5 - Cys A:6   [ RasMol ]  
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    Arg A:28 - Pro A:29   [ RasMol ]  
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    Arg D:28 - Pro D:29   [ RasMol ]  
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        PGRP1_CAMDR | Q9GK12: 2r2k 2r90 2z9n 3c2x 3cg9 3cor 3cxa 3ng4 3nno 3nw3 3o4k 3ogx 3qj1 3qs0 3qv4 3rt4 3t2v 3t39 3tru 3uil 3uml 3umq 3usx 4fnn 4opp 4orv 4oug 4q8s 4q9e 5dwf 5e0a 5e0b 5xgy

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