3C2X - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PEPTIDOGLYCAN RECOGNITION PROTEIN AT 1.8A RESOLUTION

Authors :   P. Sharma, N. Singh, M. Sinha, S. Sharma, M. Perbandt, C. Betzel, P. Kaur A. Srinivasan, T. P. Singh

Date :   26 Jan 08 (Deposition) - 25 Mar 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.83

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Antibiotic, Secretory, Immune Response, Antimicrobial, Secreted, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Sharma, N. Singh, M. Sinha, S. Sharma, M. Perbandt, C. Betzel, P. Kaur, A. Srinivasan, T. P. Singh
Crystal Structure Of The Peptidoglycan Recognition Protein At 1. 8 A Resolution Reveals Dual Strategy To Combat Infection Through Two Independent Functional Homodimers
J. Mol. Biol. V. 378 921 2008
PubMed-ID: 18395744 | Reference-DOI: 10.1016/J.JMB.2008.03.018

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

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 15)

No.	Name	Count	Type	Full Name
1	GOL	13	Ligand/Ion	GLYCEROL
2	SO4	1	Ligand/Ion	SULFATE ION
3	TLA	1	Ligand/Ion	L(+)-TARTARIC ACID

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	GOL	5	Ligand/Ion	GLYCEROL
2	SO4	-1	Ligand/Ion	SULFATE ION
3	TLA	-1	Ligand/Ion	L(+)-TARTARIC ACID

Biological Unit 2 (3, 10)

No.	Name	Count	Type	Full Name
1	GOL	8	Ligand/Ion	GLYCEROL
2	SO4	1	Ligand/Ion	SULFATE ION
3	TLA	1	Ligand/Ion	L(+)-TARTARIC ACID

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TRP C:66 , PRO D:96 , THR D:97 , GLN D:150	BINDING SITE FOR RESIDUE SO4 D 502
02	AC2	SOFTWARE	HIS C:37 , ALA C:39 , THR C:152 , LEU C:153 , SER C:154 , HIS D:37 , ALA D:39 , THR D:152 , LEU D:153 , SER D:154	BINDING SITE FOR RESIDUE TLA C 6748
03	AC3	SOFTWARE	GLY A:40 , SER A:41 , GLN A:52 , ASN A:55	BINDING SITE FOR RESIDUE GOL A 172
04	AC4	SOFTWARE	GLY B:40 , SER B:41 , GLN B:52 , ASN B:55	BINDING SITE FOR RESIDUE GOL B 172
05	AC5	SOFTWARE	HIS C:42 , ARG C:114	BINDING SITE FOR RESIDUE GOL C 6749
06	AC6	SOFTWARE	LYS C:90 , GLY C:95 , PRO C:96 , ASN C:99 , PRO C:100 , PRO D:96	BINDING SITE FOR RESIDUE GOL C 6750
07	AC7	SOFTWARE	TYR C:32 , TRP C:98	BINDING SITE FOR RESIDUE GOL C 6751
08	AC8	SOFTWARE	PRO C:151 , THR C:152 , HIS D:37 , ALA D:39 , TYR D:71 , HIS D:146	BINDING SITE FOR RESIDUE GOL D 503
09	AC9	SOFTWARE	SER A:139 , HIS A:168	BINDING SITE FOR RESIDUE GOL A 173
10	BC1	SOFTWARE	ARG A:25 , GLU A:83 , ASN A:88	BINDING SITE FOR RESIDUE GOL A 174
11	BC2	SOFTWARE	PRO C:96 , LYS D:90 , GLY D:95 , PRO D:96 , ASN D:99	BINDING SITE FOR RESIDUE GOL D 504
12	BC3	SOFTWARE	LYS A:90 , PRO A:96 , ASN A:99	BINDING SITE FOR RESIDUE GOL A 175
13	BC4	SOFTWARE	ARG D:147 , LEU D:153 , ASP D:157	BINDING SITE FOR RESIDUE GOL D 505
14	BC5	SOFTWARE	ASN A:113 , ARG D:170	BINDING SITE FOR RESIDUE GOL D 506
15	BC6	SOFTWARE	HIS D:42	BINDING SITE FOR RESIDUE GOL D 507

Asymmetric Unit

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

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 3C2X)

(no "PROSITE Motif" information available for 3C2X)

(no "Exon" information available for 3C2X)

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
 aligned with PGRP1_CAMDR | Q9GK12 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:171
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192 
          PGRP1_CAMDR    23 EDPPACGSIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQTWSHYRA 193
               SCOP domains d3c2xa_ A: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............................eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee..........hhhhhh..eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeeehhhhh.....hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c2x 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
 aligned with PGRP1_CAMDR | Q9GK12 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:171
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192 
          PGRP1_CAMDR    23 EDPPACGSIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQTWSHYRA 193
               SCOP domains d3c2xb_ B: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eehhhhhh.............eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee..........hhhhhh..eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeee..........hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c2x 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
 aligned with PGRP1_CAMDR | Q9GK12 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:171
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192 
          PGRP1_CAMDR    23 EDPPACGSIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQTWSHYRA 193
               SCOP domains d3c2xc_ 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
                 3c2x 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
 aligned with PGRP1_CAMDR | Q9GK12 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:171
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192 
          PGRP1_CAMDR    23 EDPPACGSIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCAQQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNPISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQPTLSPGDRLYEIIQTWSHYRA 193
               SCOP domains d3c2xd_ D: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhh.............eeeeeeee.......hhhhhhhhhhhhhhhhhhh.........eee.....eee..........hhhhhh..eeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeee.hhh......hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c2x 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)
		→ 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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: N-acetylmuramoyl-L-alanine amidase-like (59)

Superfamily: N-acetylmuramoyl-L-alanine amidase-like (59)

Family: N-acetylmuramoyl-L-alanine amidase-like (53)

Protein domain: automated matches (30)

Camel (Camelus dromedarius) [TaxId: 9838] (27)

1a	d3c2xa_	A:
1b	d3c2xc_	C:
1c	d3c2xd_	D:
1d	d3c2xb_	B:

(no "CATH Domain" information available for 3C2X)

(no "Pfam Domain" information available for 3C2X)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PGRP1_CAMDR | Q9GK12)

molecular function
	GO:0008745	N-acetylmuramoyl-L-alanine amidase activity	Catalysis of the hydrolysis of the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.
	GO:0042834	peptidoglycan binding	Interacting selectively and non-covalently, in a non-covalent manner, with peptidoglycan, any of a class of glycoconjugates found in bacterial cell walls.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0001818	negative regulation of cytokine production	Any process that stops, prevents, or reduces the rate of production of a cytokine.
	GO:0009253	peptidoglycan catabolic process	The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Arg A:28 - Pro A:29	[ RasMol ]
		Arg B:28 - Pro B:29	[ RasMol ]
		Arg C:28 - Pro C:29	[ RasMol ]
		Arg D:28 - Pro D:29	[ RasMol ]
		Ser A:154 - Pro A:155	[ RasMol ]
		Ser B:154 - Pro B:155	[ RasMol ]
		Ser C:154 - Pro C:155	[ RasMol ]
		Ser D:154 - Pro D:155	[ RasMol ]

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1sxr	DROSOPHILA PEPTIDOGLYCAN RECOGNITION PROTEIN (PGRP)-SA
1yck	CRYSTAL STRUCTURE OF HUMAN PEPTIDOGLYCAN RECOGNITION PROTEIN (PGRP-S)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 15)

Sites (15, 15)

SS Bonds (12, 12)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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