1WHT - JenaLib

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Title :   STRUCTURE OF THE COMPLEX OF L-BENZYLSUCCINATE WITH WHEAT SERINE CARBOXYPEPTIDASE II AT 2.0 ANGSTROMS RESOLUTION

Authors :   T. L. Bullock, S. J. Remington

Date :   07 Mar 94 (Deposition) - 22 Jun 94 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Serine Carboxypeptidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. L. Bullock, B. Branchaud, S. J. Remington
Structure Of The Complex Of L-Benzylsuccinate With Wheat Serine Carboxypeptidase Ii At 2. 0-A Resolution.
Biochemistry V. 33 11127 1994
PubMed-ID: 7727364 | Reference-DOI: 10.1021/BI00203A009
(for further references see the PDB file header)

Molecule 1 - SERINE CARBOXYPEPTIDASE II
	Chains	:	A
	EC Number	:	3.4.16.1
	Engineered	:	YES
	Organism Common	:	COMMON WHEAT
	Organism Scientific	:	TRITICUM AESTIVUM
	Organism Taxid	:	4565

Molecule 2 - SERINE CARBOXYPEPTIDASE II
	Chains	:	B
	EC Number	:	3.4.16.1
	Engineered	:	YES
	Organism Common	:	COMMON WHEAT
	Organism Scientific	:	TRITICUM AESTIVUM
	Organism Taxid	:	4565

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	BZS	1	Ligand/Ion	L-BENZYLSUCCINIC ACID
2	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
3	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 1 (4, 14)

No.	Name	Count	Type	Full Name
1	BZS	2	Ligand/Ion	L-BENZYLSUCCINIC ACID
2	FUC	2	Ligand/Ion	ALPHA-L-FUCOSE
3	NAG	8	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	NDG	2	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 2 (4, 7)

No.	Name	Count	Type	Full Name
1	BZS	1	Ligand/Ion	L-BENZYLSUCCINIC ACID
2	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
3	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:113 , HIS A:117 , HOH A:1316 , HOH A:1356 , HOH A:1368 , HOH A:1373 , HOH A:1381 , HOH A:1382 , HOH A:1386	BINDING SITE FOR RESIDUE NAG A 1131
2	AC2	SOFTWARE	TYR A:103 , NAG A:1133 , NDG A:1134 , HOH A:1358 , THR B:293	BINDING SITE FOR RESIDUE FUC A 1132A
3	AC3	SOFTWARE	THR A:22 , GLY A:27 , TYR A:103 , ASN A:105 , FUC A:1132A , NDG A:1134	BINDING SITE FOR RESIDUE NAG A 1133
4	AC4	SOFTWARE	FUC A:1132A , NAG A:1133 , THR B:293	BINDING SITE FOR RESIDUE NDG A 1134
5	AC5	SOFTWARE	ASN B:280 , GLN B:285 , ASN B:291 , GLY B:294 , MET B:296 , TYR B:298 , TRP B:300 , NAG B:2912 , HOH B:3035	BINDING SITE FOR RESIDUE NAG B 2911
6	AC6	SOFTWARE	ASN B:280 , TYR B:298 , THR B:299 , NAG B:2911 , HOH B:3035	BINDING SITE FOR RESIDUE NAG B 2912
7	AC7	SOFTWARE	ASN A:51 , GLY A:52 , GLY A:53 , CYS A:56 , GLU A:145 , SER A:146 , TYR A:147 , HOH A:1291 , HIS B:397 , GLU B:398	BINDING SITE FOR RESIDUE BZS A 430
8	ACT	UNKNOWN	ASP B:338 , HIS B:397 , SER A:146 , GLU A:145	NULL

Asymmetric Unit

No.	Residues
1	A:56	-	B:303
2	A:210	-	A:222
3	A:246	-	B:268

Asymmetric Unit

No.	Residues
1	Gln A:42	-	Pro A:43
2	Gly A:53	-	Pro A:54
3	Ser A:95	-	Pro A:96

(no "SAP(SNP)/Variant" information available for 1WHT)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CARBOXYPEPT_SER_SER	PS00131	Serine carboxypeptidases, serine active site.	CBP2_WHEAT	154-161	1	A:142-149
2	CARBOXYPEPT_SER_HIS	PS00560	Serine carboxypeptidases, histidine active site.	CBP2_WHEAT	403-420	1	B:387-404

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CARBOXYPEPT_SER_SER	PS00131	Serine carboxypeptidases, serine active site.	CBP2_WHEAT	154-161	2	A:142-149
2	CARBOXYPEPT_SER_HIS	PS00560	Serine carboxypeptidases, histidine active site.	CBP2_WHEAT	403-420	2	B:387-404

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CARBOXYPEPT_SER_SER	PS00131	Serine carboxypeptidases, serine active site.	CBP2_WHEAT	154-161	1	A:142-149
2	CARBOXYPEPT_SER_HIS	PS00560	Serine carboxypeptidases, histidine active site.	CBP2_WHEAT	403-420	1	B:387-404

(no "Exon" information available for 1WHT)

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:256
 aligned with CBP2_WHEAT | P08819 from UniProtKB/Swiss-Prot  Length:444

    Alignment length:256
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254      
          CBP2_WHEAT      5 GHAADRIARLPGQPAVDFDMYSGYITVDEGAGRSLFYLLQEAPEDAQPAPLVLWLNGGPGCSSVAYGASEELGAFRVKPRGAGLVLNEYRWNKVANVLFLDSPAGVGFSYTNTSSDIYTSGDNRTAHDSYAFLAKWFERFPHYKYRDFYIAGESYAGHYVPELSQLVHRSKNPVINLKGFMVGNGLIDDYHDYVGTFEFWWNHGIVSDDTYRRLKEACLHDSFIHPSPACDAATDVATAEQGNIDMYSLYTPVCNI  260
               SCOP domains d1wht.1 A:,B: Serine carboxypeptidase II                                                                                                                                                                                                                         SCOP domains
               CATH domains 1whtA00 A:-5-248  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee............eeeeeeeee....eeeeeee...hhhhh...eeeee...........hhhh....eee......eee...hhhhheeeee.........eeee.........hhhhhhhhhhhhhhhhhh.......eeeeeee..hhhhhhhhhhhhhh......eeeeeeee.....hhhhhhhhhhhhhh.....hhhhhhhhhhh.........hhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------CARBOXYP--------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wht A   -5 GHAADRIARLPGQPAVDFDMYSGYITVDEGAGRSLFYLLQEAPEDAQPAPLVLWLNGGPGCSSVAYGASEELGAFRVKPRGAGLVLNEYRWNKVANVLFLDSPAGVGFSYTNTSSDIYTSGDNRTAHDSYAFLAKWFERFPHYKYRDFYIAGESYAGHYVPELSQLVHRSKNPVINLKGFMVGNGLIDDYHDYVGTFEFWWNHGIVSDDTYRRLKEACLHDSFIHPSPACDAATDVATAEQGNIDMYSLYTPVCNI  248
                                     4      ||16       |25        35        45        55   |    64        74  |     83        93       103      112A||     120       130   ||  142       152       162       172       182       192       202       212       222       232       242      
                                           11|       23A                                 58A                76A                                 112A||                   134|                                                                                                               
                                            14                                                                                                   112B|                    137                                                                                                               
                                                                                                                                                  112C

Chain B from PDB  Type:PROTEIN  Length:153
 aligned with CBP2_WHEAT | P08819 from UniProtKB/Swiss-Prot  Length:444

    Alignment length:153
                                   296       306       316       326       336       346       356       366       376       386       396       406       416       426       436   
          CBP2_WHEAT    287 SYDPCTERYSTAYYNRRDVQMALHANVTGAMNYTWATCSDTINTHWHDAPRSMLPIYRELIAAGLRIWVFSGDTDAVVPLTATRYSIGALGLPTTTSWYPWYDDQEVGGWSQVYKGLTLVSVRGAGHEVPLHRPRQALVLFQYFLQGKPMPGQ  439
               SCOP domains d1wht.1 A:,B: Serine carboxypeptidase II                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Peptidase_S10-1whtB01 B:264-417                                                                                                                    ------ Pfam domains (1)
           Pfam domains (2) Peptidase_S10-1whtB02 B:264-417                                                                                                                    ------ Pfam domains (2)
         Sec.struct. author .....hhhhhhhhh.........................hhhhh.........hhhhhhhh....eeeeeee.......hhhhhhhhh......eeeeeeee...eeeeeeeee..eeeeee......hhhh.hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------CARBOXYPEPT_SER_HI------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wht B  264 SYDPCTERYSTAYYNRRDVQMALHANVTGAMNYTWATCSDTINTHWHDAPRSMLPIYRELIAAGLRIWVFSGDTDAVVPLTATRYSIGALGLPTTTSWYPWYDDQEVGGWSQVYKGLTLVSVRGAGHEVPLHRPRQALVLFQYFLQGKPMPGQ  423
                                || 275       285       295      303B     ||310       320   ||  333       343       353|      371    |  380       390       400       410       420   
                              268|                             303A|  308A||             324|                      353|          375A                                                
                               271                              303B   308B|              328                       362                                                              
                                                                        308C

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: alpha/beta-Hydrolases (971)

Superfamily: alpha/beta-Hydrolases (971)

Family: Serine carboxypeptidase-like (15)

Protein domain: Serine carboxypeptidase II (8)

Wheat (Triticum vulgare) [TaxId: 4565] (5)

d1wht.1

A:,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=3.40.50.1820, no name defined] (692)

Common wheat (Triticum aestivum) (2)

1whtA00

A:-5-248

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: AB_hydrolase (347)

Family: Peptidase_S10 (5)

Triticum aestivum (Wheat) (3)

1a	Peptidase_S10-1whtB01	B:264-417
1b	Peptidase_S10-1whtB02	B:264-417

Asymmetric Unit(hide GO term definitions)

Chain A,B (CBP2_WHEAT | P08819)

molecular function
	GO:0004180	carboxypeptidase activity	Catalysis of the hydrolysis of the terminal or penultimate peptide bond at the C-terminal end of a peptide or polypeptide.
	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: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:0004185	serine-type carboxypeptidase activity	Catalysis of the hydrolysis of a peptide bond not more than three residues from the C-terminus of 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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	CBP2_WHEAT \| P08819	:	1bcr 1bcs 1whs 3sc2

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Description

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Ligands, Modified Residues, Ions (4, 7)

Sites (8, 8)

SS Bonds (3, 3)

Cis Peptide Bonds (3, 3)

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