4TOQ - JenaLib

Title :   CRYSTAL STRUCTURE OF CLASS III CHITINASE FROM POMEGRANATE PROVIDES THE INSIGHT INTO ITS METAL STORAGE CAPACITY

Authors :   T. Masuda, G. Zhao, B. Mikami

Date :   06 Jun 14 (Deposition) - 10 Sep 14 (Release) - 04 Nov 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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 :   Chitinase, Metal Binding, A, B-Barrel, Pomegranate Seed, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Masuda, G. Zhao, B. Mikami
Crystal Structure Of Class Iii Chitinase From Pomegranate Provides The Insight Into Its Metal Storage Capacity.
Biosci. Biotechnol. Biochem. V. 79 45 2015
PubMed-ID: 25252615 | Reference-DOI: 10.1080/09168451.2014.962475

Compounds

Molecule 1 - CLASS III CHITINASE
	Chains	:	A, B, C, D
	EC Number	:	3.2.1.14
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 27-299
	Gene	:	PSC
	Organism Common	:	POMEGRANATE
	Organism Scientific	:	PUNICA GRANATUM
	Organism Taxid	:	22663

Structural Features

Chains, Units

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
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 (2, 19)

Asymmetric Unit (2, 19)

No.	Name	Count	Type	Full Name
1	CL	6	Ligand/Ion	CHLORIDE ION
2	MG	13	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Sites (19, 19)

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:50 , THR A:56 , THR C:56	binding site for residue MG A 301
02	AC2	SOFTWARE	HOH A:548 , HOH A:590 , HOH A:672 , HOH A:724 , HOH A:725	binding site for residue MG A 302
03	AC3	SOFTWARE	HOH A:625 , HOH A:727 , HOH A:728 , HOH A:744	binding site for residue MG A 303
04	AC4	SOFTWARE	HOH A:415 , HOH A:512 , HOH A:539 , HOH B:409 , HOH B:479	binding site for residue MG A 304
05	AC5	SOFTWARE	THR A:208 , SER A:248 , HOH A:408	binding site for residue MG A 305
06	AC6	SOFTWARE	ALA A:41 , ALA B:41	binding site for residue CL A 306
07	AC7	SOFTWARE	ASN A:185 , PRO A:186 , LEU A:187 , ALA A:188 , HOH A:436	binding site for residue CL A 307
08	AC8	SOFTWARE	HOH B:456 , HOH B:459 , HOH B:511 , HOH B:558	binding site for residue MG B 301
09	AC9	SOFTWARE	HOH B:596 , HOH B:692 , HOH B:696	binding site for residue MG B 302
10	AD1	SOFTWARE	HIS B:49	binding site for residue CL B 303
11	AD2	SOFTWARE	GLY B:11 , ALA B:47 , GLY B:48 , GLY D:11	binding site for residue CL B 304
12	AD3	SOFTWARE	ASN B:185 , PRO B:186 , LEU B:187 , HOH B:444	binding site for residue CL B 305
13	AD4	SOFTWARE	PRO C:52 , GLY C:55 , THR C:56 , CYS C:57 , PRO C:113	binding site for residue MG C 301
14	AD5	SOFTWARE	HOH A:432 , HOH C:427 , HOH C:713	binding site for residue MG C 302
15	AD6	SOFTWARE	HOH C:513 , HOH C:577 , HOH C:578 , HOH C:645 , HOH C:662	binding site for residue MG C 303
16	AD7	SOFTWARE	HOH C:552 , HOH C:607 , HOH C:625 , HOH C:650 , HOH C:651	binding site for residue MG C 304
17	AD8	SOFTWARE	ARG C:144 , HOH C:548 , ASN D:102 , HOH D:613	binding site for residue CL C 305
18	AD9	SOFTWARE	ARG A:65 , THR C:146 , GLN C:147 , ALA C:148 , HOH C:484 , SER D:110	binding site for residue MG D 301
19	AE1	SOFTWARE	HOH D:602 , HOH D:641 , HOH D:697 , HOH D:708 , HOH D:709	binding site for residue MG D 302

SS Bonds (12, 12)

Asymmetric Unit

No.	Residues
1	A:20	-	A:67
2	A:50	-	A:57
3	A:159	-	A:190
4	B:20	-	B:67
5	B:50	-	B:57
6	B:159	-	B:190
7	C:20	-	C:67
8	C:50	-	C:57
9	C:159	-	C:190
10	D:20	-	D:67
11	D:50	-	D:57
12	D:159	-	D:190

Cis Peptide Bonds (12, 13)

Asymmetric Unit

No.	Residues
1	Ser A:31	-	Phe A:32
2	His A:161	-	Pro A:162
3	Tyr A:257	-	Ser A:258
4	Ser B:31	-	Phe B:32
5	His B:161	-	Pro B:162
6	Tyr B:257	-	Ser B:258
7	Ser C:31	-	Phe C:32
8	His C:161	-	Pro C:162
9	Tyr C:257	-	Ser C:258
10	Ser D:31	-	Phe D:32
11	His D:161	-	Pro D:162
12	Tyr D:257	-	Ser D:258

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:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhh....eeeeeeeeeee..eeeee......hhhhh...hhhhhhhhhhh...eeeeeee....ee...hhhhhhhhhhhhhhhhh...............eeeee.......hhhhhhhhhhh........eeee..........hhhhhh.....eeeee...............hhhhhhhhhhhhhhh...eeeeeee.hhhhh.....hhhhhhhhhhhhhh....eeeeeeehhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4toq A   1 GDIAIYWGQNGGEGTLASTCDTGRYAYVIVSFVTTFGNFRAPVVNLAGHCDPAAGTCTGLSDEIRSCQGKDIKVLMSIGGGAGDYSLVSEADADNFADYLWNNFLGGQSSSRPLGDAVLDGIDFDIELGTTTFYDTLARALSSRSTQAAKVYLTAAPQCPHPDSHLDAALNTGLFDNVWIQFYNNPLAQCQYSSGNTNDILSSWNTWTSSTTAGKIFLGLPAAPEAAGSGYIPPDVLTGQILPQIKTSAKYGGVMLYSKFYDTTYSTTIKDQV 273
                                    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

Chain B from PDB  Type:PROTEIN  Length:270
                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.......hhhhhhhh....eeeeeeeeee......ee......hhhhh...hhhhhhhhhhhh..eeeeeee....ee...hhhhhhhhhhhhhhhhh...............eeeee.......hhhhhhhhhhhhh...eeee..........hhhhhh.....eeeee...............hhhhhhhhhhhhhh....eeeeeee.hhhhh.....hhhhhhhhhhhhhh....eeeeeeehhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4toq B   1 GDIAIYWGQNGGEGTLASTCDTGRYAYVIVSFVTTFGNFRAPVVNLAGHCDPAAGTCTGLSDEIRSCQGKDIKVLMSIGGGAGDYSLVSEADADNFADYLWNNFLGGQSSSRPLGDAVLDGIDFDIELGTTTFYDTLARALSSRSAKVYLTAAPQCPHPDSHLDAALNTGLFDNVWIQFYNNPLAQCQYSSGNTNDILSSWNTWTSSTTAGKIFLGLPAAPEAAGSGYIPPDVLTGQILPQIKTSAKYGGVMLYSKFYDTTYSTTIKDQV 273
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    || 153       163       173       183       193       203       213       223       233       243       253       263       273
                                                                                                                                                                          145|                                                                                                                            
                                                                                                                                                                           149

Chain C from PDB  Type:PROTEIN  Length:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......hhhhhhhh....eeeeeeeeee......ee..............hhhhhhhhhhhh..eeeeeee....ee...hhhhhhhhhhhhhhhhh...............eeeee.......hhhhhhhhhhh........eeee..........hhhhhh.....eeeee...............hhhhhhhhhhhhh.....eeeeeee.hhhhh.....hhhhhhhhhhhhhh....eeeeeeehhhhh.hhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4toq C   1 GDIAIYWGQNGGEGTLASTCDTGRYAYVIVSFVTTFGNFRAPVVNLAGHCDPAAGTCTGLSDEIRSCQGKDIKVLMSIGGGAGDYSLVSEADADNFADYLWNNFLGGQSSSRPLGDAVLDGIDFDIELGTTTFYDTLARALSSRSTQAAKVYLTAAPQCPHPDSHLDAALNTGLFDNVWIQFYNNPLAQCQYSSGNTNDILSSWNTWTSSTTAGKIFLGLPAAPEAAGSGYIPPDVLTGQILPQIKTSAKYGGVMLYSKFYDTTYSTTIKDQV 273
                                    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

Chain D from PDB  Type:PROTEIN  Length:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......hhhhhhhh....eeeeeeeeee......ee..............hhhhhhhhhhh...eeeeeee....ee...hhhhhhhhhhhhhhhh................eeeee.......hhhhhhhhhhh........eeee..........hhhhhhh....eeeee...............hhhhhhhhhhhhh.....eeeeeee...........hhhhhhhhhhhhhh....eeeeeeehhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4toq D   1 GDIAIYWGQNGGEGTLASTCDTGRYAYVIVSFVTTFGNFRAPVVNLAGHCDPAAGTCTGLSDEIRSCQGKDIKVLMSIGGGAGDYSLVSEADADNFADYLWNNFLGGQSSSRPLGDAVLDGIDFDIELGTTTFYDTLARALSSRSTQAAKVYLTAAPQCPHPDSHLDAALNTGLFDNVWIQFYNNPLAQCQYSSGNTNDILSSWNTWTSSTTAGKIFLGLPAAPEAAGSGYIPPDVLTGQILPQIKTSAKYGGVMLYSKFYDTTYSTTIKDQV 273
                                    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

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SCOP Domains (0, 0)

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Pfam Domains (0, 0)

Gene Ontology (6, 6)

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 19)

Sites (19, 19)

SS Bonds (12, 12)

Cis Peptide Bonds (12, 13)

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