3D43 - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF SPH AT 0.8A

Authors :   O. Almog

Date :   13 May 08 (Deposition) - 28 Apr 09 (Release) - 28 Apr 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   0.80

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

Keywords :   Serin Protease, Calcium Binding, Hydrolase, Serine Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Almog, A. Gonzalez, N. Godin, M. De Leeuw, M. J. Mekel, D. Klein, S. Braun, G. Shoham, R. L. Walter
The Crystal Structures Of The Psychrophilic Subtilisin S41 And The Mesophilic Subtilisin Sph Reveal The Same Calcium-Loaded State.
Proteins V. 74 489 2009
PubMed-ID: 18655058 | Reference-DOI: 10.1002/PROT.22175
(for further references see the PDB file header)

Molecule 1 - SPHERICASE
	Chains	:	A, B
	Organism Scientific	:	BACILLUS SPHAERICUS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 10)

No.	Name	Count	Type	Full Name
1	CA	10	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:287 , ILE A:288 , ALA A:295 , GLY A:297 , ASP A:299	BINDING SITE FOR RESIDUE CA A 312
02	AC2	SOFTWARE	THR A:214 , ASP A:217 , GLN A:221 , ASP A:224	BINDING SITE FOR RESIDUE CA A 313
03	AC3	SOFTWARE	ASN A:29 , GLU A:49 , ASP A:98	BINDING SITE FOR RESIDUE CA A 314
04	AC4	SOFTWARE	ASP A:115	BINDING SITE FOR RESIDUE CA A 315
05	AC5	SOFTWARE	GLY A:181 , ALA A:182 , LEU A:183 , ALA A:186	BINDING SITE FOR RESIDUE CA A 316
06	AC6	SOFTWARE	ASP B:287 , ILE B:288 , ALA B:295 , GLY B:297 , ASP B:299	BINDING SITE FOR RESIDUE CA B 312
07	AC7	SOFTWARE	THR B:214 , ASP B:217 , GLN B:221 , ASP B:224	BINDING SITE FOR RESIDUE CA B 313
08	AC8	SOFTWARE	ASN B:29 , GLU B:49 , ASP B:98	BINDING SITE FOR RESIDUE CA B 314
09	AC9	SOFTWARE	ASP B:115	BINDING SITE FOR RESIDUE CA B 315
10	BC1	SOFTWARE	GLY B:181 , ALA B:182 , LEU B:183 , ALA B:186	BINDING SITE FOR RESIDUE CA B 316

Asymmetric Unit

No.	Residues
1	A:51	-	A:65
2	B:51	-	B:65

Asymmetric Unit

No.	Residues
1	Thr A:59	-	Pro A:60
2	Gly A:171	-	Tyr A:172
3	Tyr A:179	-	Pro A:180
4	Thr B:59	-	Pro B:60
5	Gly B:171	-	Tyr B:172
6	Tyr B:179	-	Pro B:180

(no "SAP(SNP)/Variant" information available for 3D43)

(no "PROSITE Motif" information available for 3D43)

(no "Exon" information available for 3D43)

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:309
 aligned with Q9S3L6_LYSSH | Q9S3L6 from UniProtKB/TrEMBL  Length:431

    Alignment length:309
                                   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421         
         Q9S3L6_LYSSH   122 RASQQIPWGIKAIYNNDTLTSTTGGSGINIAVLDTGVNTSHPDLVNNVEQCKDFTGATTPINNSCTDRNGHGTHVAGTALADGGSDQAGIYGVAPDADLWAYKVLLDSGSGYSDDIAAAIRHAADQATATGTKTIISMSLGSSANNSLISSAVNYAYSKGVLIVAAAGNSGYSQGTIGYPGALPNAIAVAALENVQQNGTYRVADYSSRGYISTAGDYVIQEGDIEISAPGSSVYSTWYNGGYNTISGTSMATPHVSGLAAKIWAENPSLSNTQLRSNLQERAKSVDIKGGYGAAIGDDYASGFGFARV 430
               SCOP domains d3d43a_ A: automated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3d43A00 A:1-309  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh.............eeeeee.............eeeeee.......ee.......hhhhhhhhhhhh................eeeeee........hhhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhh..eeeee....................eeeeeeeeeee..eeee.......................eeee...eeee.....eeee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...................ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d43 A   1 RASQQIPWGIKAIYNNDTLTSTTGGSGINIAVLDTGVNTSHPDLVNNVEQCKDFTGATTPINNSCTDRNGHGTHVAGTALADGGSDQAGIYGVAPDADLWAYKVLLDSGSGYSDDIAAAIRHAADQATATGTKTIISMSLGSSANNSLISSAVNYAYSKGVLIVAAAGNSGYSQGTIGYPGALPNAIAVAALENVQQNGTYRVADYSSRGYISTAGDYVIQEGDIEISAPGSSVYSTWYNGGYNTISGTSMATPHVSGLAAKIWAENPSLSNTQLRSNLQERAKSVDIKGGYGAAIGDDYASGFGFARV 309
                                    10        20        30        40        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

Chain B from PDB  Type:PROTEIN  Length:310
 aligned with Q9S3L6_LYSSH | Q9S3L6 from UniProtKB/TrEMBL  Length:431

    Alignment length:310
                                   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431
         Q9S3L6_LYSSH   122 RASQQIPWGIKAIYNNDTLTSTTGGSGINIAVLDTGVNTSHPDLVNNVEQCKDFTGATTPINNSCTDRNGHGTHVAGTALADGGSDQAGIYGVAPDADLWAYKVLLDSGSGYSDDIAAAIRHAADQATATGTKTIISMSLGSSANNSLISSAVNYAYSKGVLIVAAAGNSGYSQGTIGYPGALPNAIAVAALENVQQNGTYRVADYSSRGYISTAGDYVIQEGDIEISAPGSSVYSTWYNGGYNTISGTSMATPHVSGLAAKIWAENPSLSNTQLRSNLQERAKSVDIKGGYGAAIGDDYASGFGFARVQ 431
               SCOP domains d3d43b_ B: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3d43B00 B:1-310  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh.............eeeeee.............eeeeee.......ee.......hhhhhhhhhhhh................eeeeee........hhhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhh..eeeee....................eeeeeeeeeee..eeee.......................eeee...eeee.....eeee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d43 B   1 RASQQIPWGIKAIYNNDTLTSTTGGSGINIAVLDTGVNTSHPDLVNNVEQCKDFTGATTPINNSCTDRNGHGTHVAGTALADGGSDQAGIYGVAPDADLWAYKVLLDSGSGYSDDIAAAIRHAADQATATGTKTIISMSLGSSANNSLISSAVNYAYSKGVLIVAAAGNSGYSQGTIGYPGALPNAIAVAALENVQQNGTYRVADYSSRGYISTAGDYVIQEGDIEISAPGSSVYSTWYNGGYNTISGTSMATPHVSGLAAKIWAENPSLSNTQLRSNLQERAKSVDIKGGYGAAIGDDYASGFGFARVQ 310
                                    10        20        30        40        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

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) (23833)

Fold: Subtilisin-like (227)

Superfamily: Subtilisin-like (227)

Family: Subtilases (190)

Protein domain: automated matches (58)

Bacillus sphaericus [TaxId: 1421] (2)

1a	d3d43a_	A:
1b	d3d43b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.200, no name defined] (198)

Bacillus sphaericus (1)

1a	3d43A00	A:1-309
1b	3d43B00	B:1-310

(no "Pfam Domain" information available for 3D43)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q9S3L6_LYSSH | Q9S3L6)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:171 - Tyr A:172	[ RasMol ]
		Gly B:171 - Tyr B:172	[ RasMol ]
		Thr A:59 - Pro A:60	[ RasMol ]
		Thr B:59 - Pro B:60	[ RasMol ]
		Tyr A:179 - Pro A:180	[ RasMol ]
		Tyr B:179 - Pro B:180	[ RasMol ]

Biological Units
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Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 10)

Sites (10, 10)

SS Bonds (2, 2)

Cis Peptide Bonds (6, 6)

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