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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF CAMEL PEPTIDOGLYCAN RECOGNITION PROTEIN PGRP-S WITH 7- PHENYLHEPTANOIC ACID AND N-ACETYLGLUCOSAMINE AT 2.50 A RESOLUTION
 
Authors :  S. Yamini, P. Sharma, S. P. Yadav, M. Sinha, A. Bhushan, P. Kaur, S. Sharm T. P. Singh
Date :  12 Feb 14  (Deposition) - 05 Mar 14  (Release) - 05 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Immune Response, Secreted, Antimicrobial, Pgrp-S, Antibiotic, Peptidoglycan Binding, Immune System', Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Yamini, P. Sharma, S. P. Yadav, M. Sinha, A. Bhushan, P. Kaur, S. Sharma, T. P. Singh
Crystal Structure Of The Ternary Complex Of Camel Peptidoglycan Recognition Protein Pgrp-S With 7- Phenylheptanoic Acid And N- Acetylglucosamine At 2. 50 A Resolution
To Be Published
PubMed: search

(-) Compounds

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

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3TLA1Ligand/IonL(+)-TARTARIC ACID
4XXC2Ligand/Ion7-PHENYLHEPTANOIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2NAG-1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3TLA-1Ligand/IonL(+)-TARTARIC ACID
4XXC1Ligand/Ion7-PHENYLHEPTANOIC ACID
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3TLA1Ligand/IonL(+)-TARTARIC ACID
4XXC1Ligand/Ion7-PHENYLHEPTANOIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:6 , ASN A:126 , PRO B:4 , ARG D:138BINDING SITE FOR RESIDUE XXC B 201
2AC2SOFTWAREHIS C:37 , ALA C:39 , THR C:152 , LEU C:153 , HIS D:37 , ALA D:39 , THR D:152 , LEU D:153 , SER D:154 , GOL D:201BINDING SITE FOR RESIDUE TLA C 201
3AC3SOFTWARETRP C:66 , GLY C:91 , ALA C:92 , PRO C:96 , ASN C:99 , THR D:97 , GLN D:150BINDING SITE FOR RESIDUE NAG C 202
4AC4SOFTWAREPRO C:151 , TLA C:201 , HIS D:37 , THR D:38 , ALA D:39 , TYR D:71 , HIS D:146 , HOH D:302 , HOH D:341BINDING SITE FOR RESIDUE GOL D 201
5AC5SOFTWAREPRO C:96 , GLN C:150 , TRP D:66 , ARG D:85 , ALA D:92 , HIS D:93 , GLY D:95 , ASN D:99 , HOH D:370BINDING SITE FOR RESIDUE XXC D 202

(-) SS Bonds  (12, 12)

Asymmetric 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  (9, 9)

Asymmetric Unit
No.Residues
1Arg A:28 -Pro A:29
2Ser A:154 -Pro A:155
3Glu B:1 -Asp B:2
4Arg B:28 -Pro B:29
5Ser B:154 -Pro B:155
6Arg C:28 -Pro C:29
7Ser C:154 -Pro C:155
8Arg D:28 -Pro D:29
9Ser D:154 -Pro D:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ORV)

(-) 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:171
                                                                                                                                                                                                           
               SCOP domains d4orva_ A: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhh.............eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee..................eeeeee.........hhhhhhhhhhhhhhhhhhh.eeeeeeeeehhhhh.....hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4orv 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 d4orvb_ B: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eehhhhhh.............eeeeeeee.......hhhhhhhhhhhhhhhhhh..........eee.....eee..........hhhhhh..eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeee.hhh......hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4orv 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 d4orvc_ C: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eehhhhhh.............eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee..............hhh.eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeee.hhh......hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4orv 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 d4orvd_ D: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee.hhhhh.............eeeeeeee.......hhhhhhhhhhhhhhhhhh..........eee.....eee..............hhh.eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeee.hhh......hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4orv 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)
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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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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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 4gf9 4opp 4oug 4q8s 4q9e 5dwf 5e0a 5e0b 5xgy

(-) Related Entries Specified in the PDB File

3c2x