4RNY - JenaLib

Title :   STRUCTURE OF HELICOBACTER PYLORI CSD3 FROM THE ORTHORHOMBIC CRYSTAL

Authors :   D. R. An, H. S. Kim, J. Kim, H. N. Im, H. J. Yoon, J. Y. Yoon, J. Y. Jang, D. Hes S. Mobashery, S. -J. Kim, B. I. Lee, S. W. Suh

Date :   27 Oct 14 (Deposition) - 11 Mar 15 (Release) - 25 Mar 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   M23B Metallopeptidase, Metallopeptidase, Peptidoglycan, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. R. An, H. S. Kim, J. Kim, H. N. Im, H. J. Yoon, J. Y. Yoon, J. Y. Jang, D. Hesek, M. Lee, S. Mobashery, S. J. Kim, B. I. Lee, S. W. Suh
Structure Of Csd3 From Helicobacter Pylori, A Cell Shape-Determining Metallopeptidase.
Acta Crystallogr. , Sect. D V. 71 675 2015
PubMed-ID: 25760614 | Reference-DOI: 10.1107/S1399004715000152

Compounds

Molecule 1 - CONSERVED HYPOTHETICAL SECRETED PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 42-403
	Gene	:	C694_02600, HP_0506
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	85962
	Strain	:	ATCC 700392 / 26695
	Synonym	:	CSD3 CELL-SHAPE DETERMINANT

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 16)

Asymmetric Unit (3, 16)

No.	Name	Count	Type	Full Name
1	GOL	5	Ligand/Ion	GLYCEROL
2	SO4	9	Ligand/Ion	SULFATE ION
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	SO4	4	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SO4	5	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (2, 14)

No.	Name	Count	Type	Full Name
1	GOL	5	Ligand/Ion	GLYCEROL
2	SO4	9	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Sites (16, 16)

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:74 , HIS A:259 , ASP A:263 , HIS A:341	BINDING SITE FOR RESIDUE ZN A 501
02	AC2	SOFTWARE	GLN A:104 , ASP A:105 , PHE A:126 , ARG A:128 , ASP A:184 , ARG A:349 , HOH A:628 , HIS B:250 , PRO B:251 , VAL B:252	BINDING SITE FOR RESIDUE SO4 A 502
03	AC3	SOFTWARE	TYR A:208 , TYR A:209 , ASP A:220 , SER A:221 , ARG B:43	BINDING SITE FOR RESIDUE SO4 A 503
04	AC4	SOFTWARE	ASN A:82 , THR A:84 , PHE A:191 , GLY A:192 , HOH A:633 , ARG B:170	BINDING SITE FOR RESIDUE SO4 A 504
05	AC5	SOFTWARE	HIS A:390 , LEU A:400	BINDING SITE FOR RESIDUE SO4 A 505
06	AC6	SOFTWARE	SER A:245 , TYR A:246 , ARG A:256 , GOL A:509 , ARG B:248 , LYS B:254	BINDING SITE FOR RESIDUE GOL A 506
07	AC7	SOFTWARE	THR A:50 , LEU A:51 , LEU A:52 , ALA A:287	BINDING SITE FOR RESIDUE GOL A 507
08	AC8	SOFTWARE	SER A:103 , GLN A:104 , ASP A:105 , TYR A:246 , ARG A:349 , PRO A:350 , ILE A:351 , HOH A:612 , HOH A:664	BINDING SITE FOR RESIDUE GOL A 508
09	AC9	SOFTWARE	ASN A:215 , ASN A:352 , GOL A:506 , LYS B:254	BINDING SITE FOR RESIDUE GOL A 509
10	BC1	SOFTWARE	GLU B:74 , HIS B:259 , ASP B:263 , HIS B:341	BINDING SITE FOR RESIDUE ZN B 501
11	BC2	SOFTWARE	ARG A:248 , PHE A:249 , HIS A:250 , ARG B:248 , PHE B:249 , HIS B:250 , HOH B:622	BINDING SITE FOR RESIDUE SO4 B 502
12	BC3	SOFTWARE	HIS A:250 , PRO A:251 , VAL A:252 , GLN B:104 , ASP B:105 , PHE B:126 , ARG B:128 , ASP B:184 , ARG B:349 , HOH B:640	BINDING SITE FOR RESIDUE SO4 B 503
13	BC4	SOFTWARE	ARG A:170 , ARG A:204 , VAL B:83 , THR B:84 , GLY B:192 , HOH B:626 , HOH B:693	BINDING SITE FOR RESIDUE SO4 B 504
14	BC5	SOFTWARE	HIS B:390 , LEU B:400	BINDING SITE FOR RESIDUE SO4 B 505
15	BC6	SOFTWARE	TYR B:208 , TYR B:209 , ASP B:220 , SER B:221	BINDING SITE FOR RESIDUE SO4 B 506
16	BC7	SOFTWARE	LYS A:254 , ASN B:352 , HOH B:680	BINDING SITE FOR RESIDUE GOL B 507

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:359
                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhh...hhhhhh.hhhhhhhhh......eeeeee.....eeeeeee....eeeeeeee..eeeeeeee...eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh....hhhhh....eeeeeeeeeee..eeeeeeeeeeeeeee..eeeeeee.....ee.....ee............eeee........hhhhh......eeee.....eee....eeeeeeeee...eeeeeeee..eeeeeeeeeee........ee....eeeee.....eeeeeeee..eeehhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rny A  41 MERLVWDKLTLLGFLEKNHIPQKLYYNLSSQDKELSAEIQSNVTYYTLRDANNTLIQALIPISQDLQIHIYKKGEDYFLDFIPIIFTRKEKTLLLSLQTSPYQDIIKATNDPLLANQLMNAYKKSVPFKRLVKNDKIAIVYTRDYRVGQAFGQPTIKMAMVSSRSNQYYLFSHSNGHYYDSKAQEVAGFLLETPVKYTRISSPFSYGRFHPVLKVRRPHYGVDYAAKHGSLIHSASDGRVGFMGVKAGYGKVVEIHLNELRLVYAHMSAFANGLKKGSFVKKGQIIGRVGSTGPHLHFGVYKNSRPINPLGYIRTAKSKLHGKQREVFLEKAQRSKQKLEELLKTHSFEKNSFYLLEGF 403
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330 ||    344       354       364       374       384       394         
                                                                                                                                                                                                                                                                                                                             332|                                                                  
                                                                                                                                                                                                                                                                                                                              337

Chain B from PDB  Type:PROTEIN  Length:359
                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhh...hhhhhh.hhhhhhhhh......eeeeee.....eeeeeee....eeeeeeee..eeeeeeee...eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh....hhhhh....eeeeeeeeeee..eeeeeeeeeeeeeee..eeeeee......ee.....ee............eeee........hhhhh......eeee.....eee....eeeeeeeee...eeeeeeee..eeeeeeeeeee........ee....eeeee.....eeeeeeee..eeehhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rny B  41 MERLVWDKLTLLGFLEKNHIPQKLYYNLSSQDKELSAEIQSNVTYYTLRDANNTLIQALIPISQDLQIHIYKKGEDYFLDFIPIIFTRKEKTLLLSLQTSPYQDIIKATNDPLLANQLMNAYKKSVPFKRLVKNDKIAIVYTRDYRVGQAFGQPTIKMAMVSSRSNQYYLFSHSNGHYYDSKAQEVAGFLLETPVKYTRISSPFSYGRFHPVLKVRRPHYGVDYAAKHGSLIHSASDGRVGFMGVKAGYGKVVEIHLNELRLVYAHMSAFANGLKKGSFVKKGQIIGRVGSTGPHLHFGVYKNSRPINPLGYIRTAKSKLHGKQREVFLEKAQRSKQKLEELLKTHSFEKNSFYLLEGF 403
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330 ||    344       354       364       374       384       394         
                                                                                                                                                                                                                                                                                                                             332|                                                                  
                                                                                                                                                                                                                                                                                                                              337

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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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (3, 3)

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