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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX OF PEPTIDOGLYCAN RECOGNITION PROTEIN, PGRP-S FROM CAMEL WITH ETHYLENE GLYCOL AT 1.83 A RESOLUTION
 
Authors :  P. K. Singh, S. P. Yadav, P. Sharma, P. Kaur, S. Sharma, T. P. Singh
Date :  22 Sep 15  (Deposition) - 14 Oct 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Pgrp, Complex, Ethylene Glycol, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. K. Singh, S. P. Yadav, P. Sharma, P. Kaur, S. Sharma, T. P. Singh
Crystal Structure Of The Complex Of Peptidoglycan Recognition Protein, Pgrp-S From Camel With Ethylene Glycol At 1. 83 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEPTIDOGLYCAN RECOGNITION PROTEIN 1
    Chains: A, B, C, D
    Engineered: YES
    Expression System: CAMELUS DROMEDARIUS
    Expression System Common: CAMEL
    Expression System Taxid: 9838
    Fragment: UNP RESIDUES 28-193
    Gene: PGLYRP1, PGLYRP, PGRP
    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): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3TLA1Ligand/IonL(+)-TARTARIC ACID
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2GOL-1Ligand/IonGLYCEROL
3TLA-1Ligand/IonL(+)-TARTARIC ACID
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2GOL-1Ligand/IonGLYCEROL
3TLA-1Ligand/IonL(+)-TARTARIC ACID
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2GOL-1Ligand/IonGLYCEROL
3TLA1Ligand/IonL(+)-TARTARIC ACID
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3TLA-1Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS C:37 , THR C:152 , LEU C:153 , SER C:154 , HIS D:37 , ALA D:39 , THR D:152 , LEU D:153 , SER D:154 , GOL D:201binding site for residue TLA C 201
2AC2SOFTWAREALA C:50 , HOH C:335binding site for residue EDO C 202
3AC3SOFTWAREPRO C:151 , THR C:152 , TLA C:201 , HIS D:37 , THR D:38 , ALA D:39 , TYR D:71 , HIS D:146 , HOH D:309binding site for residue GOL D 201
4AC4SOFTWAREHOH A:250 , TYR D:32 , HOH D:333 , HOH D:348binding site for residue EDO 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  (10, 10)

Asymmetric Unit
No.Residues
1Arg A:28 -Pro A:29
2Ser A:154 -Pro A:155
3Cys B:6 -Gly B:7
4Arg B:28 -Pro B:29
5Ala B:133 -Leu B:134
6Ser B:154 -Pro B:155
7Arg C:28 -Pro C:29
8Ser C:154 -Pro C:155
9Arg D:28 -Pro D:29
10Ser D:154 -Pro D:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DWF)

(-) 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:166
                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhh.............eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee..........hhhhhh..eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeeehhhhh.....hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dwf A   6 CGSIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQTWSHYRA 171
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165      


Chain B from PDB  Type:PROTEIN  Length:166
                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhh.............eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee..........hhhhhh..eeeeee.........hhhhhhhhhhhhhhhhh...eeeeeeeeehhhhh.....hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dwf B   6 CGSIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQTWSHYRA 171
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165      


Chain C from PDB  Type:PROTEIN  Length:166
                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhh.............eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee..........hhhhhh..eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeee.hhh......hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dwf C   6 CGSIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQTWSHYRA 171
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165      


Chain D from PDB  Type:PROTEIN  Length:166
                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhh.............eeeeeeee.......hhhhhhhhhhhhhhhhh...........eee.....eee..........hhhhhh..eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeee.hhh......hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dwf D   6 CGSIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQTWSHYRA 171
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165
   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  (0, 0)

(no "SCOP Domain" information available for 5DWF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

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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 4orv 4oug 4q8s 4q9e 5e0a 5e0b 5xgy

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