4HPG - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A GLYCOSYLATED BETA-1,3-GLUCANASE (HEV B 2), AN ALLERGEN FROM HEVEA BRASILIENSIS

Authors :   A. Rodriguez-Romero, A. Hernandez-Santoyo

Date :   23 Oct 12 (Deposition) - 27 Nov 13 (Release) - 19 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.54

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: B  (1x)
Biol. Unit 2: C  (1x)
Biol. Unit 3: A  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Allergen, Glycoprotein, Glycoside Hydrolase, Gh17 Family, Pathogenesis-Related Class-2 Protein, Tim Barrel, Glycosidase Hydrolase, Carbohydrate/Sugar Binding, Glycosylation, Pyroglutamic Acid (N-Terminal Residue), Latex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Rodriguez-Romero, A. Hernandez-Santoyo, D. Fuentes-Silva, L. A. Palomares, S. Munoz-Cruz, L. Yepez-Mulia, S. Orozco-Martinez
Structural Analysis Of The Endogenous Glycoallergen Hev B 2 (Endo-Beta-1, 3-Glucanase) From Hevea Brasiliensis And Its Recognition By Human Basophils.
Acta Crystallogr. , Sect. D V. 70 329 2014
PubMed-ID: 24531467 | Reference-DOI: 10.1107/S1399004713027673
(for further references see the PDB file header)

Molecule 1 - BETA-1,3-GLUCANASE
	Chains	:	A, B, C, D
	EC Number	:	3.2.1.39
	Organism Common	:	PARA RUBBER TREE,JEBE,RUBBERTREE,SIRINGA
	Organism Scientific	:	HEVEA BRASILIENSIS
	Organism Taxid	:	3981
	Other Details	:	PARA RUBBER TREE LATEX
	Strain	:	GV-42

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 11)

No.	Name	Count	Type	Full Name
1	FUC	2	Ligand/Ion	ALPHA-L-FUCOSE
2	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	PCA	4	Mod. Amino Acid	PYROGLUTAMIC ACID
4	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
4	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 2 (4, 5)

No.	Name	Count	Type	Full Name
1	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	FUC	-1	Ligand/Ion	ALPHA-L-FUCOSE
2	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	FUC	-1	Ligand/Ion	ALPHA-L-FUCOSE
2	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
4	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:233 , ARG A:274	BINDING SITE FOR RESIDUE PEG A 401
2	AC2	SOFTWARE	PCA B:1 , ASN B:27 , SER B:316 , FUC B:402 , LYS C:291	BINDING SITE FOR RESIDUE NAG B 401
3	AC3	SOFTWARE	NAG B:401	BINDING SITE FOR RESIDUE FUC B 402
4	AC4	SOFTWARE	ASN C:27 , FUC C:402	BINDING SITE FOR RESIDUE NAG C 401
5	AC5	SOFTWARE	NAG C:401	BINDING SITE FOR RESIDUE FUC C 402
6	AC6	SOFTWARE	LYS C:268 , ASN C:314 , SER C:316	BINDING SITE FOR RESIDUE NAG C 403
7	AC7	SOFTWARE	TRP A:205 , TYR C:144 , TYR C:194	BINDING SITE FOR RESIDUE PEG C 404

(no "SS Bond" information available for 4HPG)

Asymmetric Unit

No.	Residues
1	Tyr A:144	-	Pro A:145
2	Phe A:284	-	Ala A:285
3	Gln A:293	-	Pro A:294
4	Tyr B:144	-	Pro B:145
5	Phe B:284	-	Ala B:285
6	Gln B:293	-	Pro B:294
7	Tyr C:144	-	Pro C:145
8	Phe C:284	-	Ala C:285
9	Gln C:293	-	Pro C:294
10	Tyr D:144	-	Pro D:145
11	Phe D:284	-	Ala D:285
12	Gln D:293	-	Pro D:294

(no "SAP(SNP)/Variant" information available for 4HPG)

(no "PROSITE Motif" information available for 4HPG)

(no "Exon" information available for 4HPG)

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:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4hpga_ A: automated matches                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.........hhhhhhhhhhhh...eee....hhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhhhhh........eeeeeeee........hhhhhhhhhhhhhhhhhhhhhh......eeeeeehhh.eee..hhhhhee...hhhhhhhhhhhhhhhh..eeee.hhhhhhhhh....hhhhhh.......eee..eee.hhhhhhhhhhhhhhhhh......eeeeee..........hhhhhhhhhhhhhhhh.............eee..........hhhhhh................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hpg A   1 xVGVCYGMQGNNLPPVSEVIALYKKSNITRMRIYDPNQAVLEALRGSNIELILGVPNSDLQSLTNPSNAKSWVQKNVRGFWSSVRFRYIAVGNEISPVNRGTAWLAQFVLPAMRNIHDAIRSAGLQDQIKVSTAIDLTLVGNSYPPSAGAFRDDVRSYLNPIIRFLSSIRSPLLANIYPYFTYAGNPRDISLPYALFTSPSVVVWDGQRGYKNLFDATLDALYSALERASGGSLEVVVSESGWPSAGAFAATFDNGRTYLSNLIQHVKRGTPKRPKRAIETYLFAMFDENKKQPEVEKHFGLFFPNKWQKYNLNFS 316
                            |       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      
                            |                                                                                                                                                                                                                                                                                                                           
                            1-PCA

Chain B from PDB  Type:PROTEIN  Length:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4hpgb_ B: automated matches                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.........hhhhhhhhhhhh...eeee...hhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeee........hhhhhhhhhhhhhhhhhhhhhh......eeeeeehhh.eee..hhhhhee...hhhhhhhhhhhhhhhh..eeee.hhhhhhhhh....hhhhhhh......eee..eee.hhhhhhhhhhhhhhhhh......eeeeee..........hhhhhhhhhhhhhhhh.............eee..........hhhhhh................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hpg B   1 xVGVCYGMQGNNLPPVSEVIALYKKSNITRMRIYDPNQAVLEALRGSNIELILGVPNSDLQSLTNPSNAKSWVQKNVRGFWSSVRFRYIAVGNEISPVNRGTAWLAQFVLPAMRNIHDAIRSAGLQDQIKVSTAIDLTLVGNSYPPSAGAFRDDVRSYLNPIIRFLSSIRSPLLANIYPYFTYAGNPRDISLPYALFTSPSVVVWDGQRGYKNLFDATLDALYSALERASGGSLEVVVSESGWPSAGAFAATFDNGRTYLSNLIQHVKRGTPKRPKRAIETYLFAMFDENKKQPEVEKHFGLFFPNKWQKYNLNFS 316
                            |       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      
                            1-PCA

Chain C from PDB  Type:PROTEIN  Length:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4hpgc_ C: automated matches                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.........hhhhhhhhhhhh...eeee...hhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeee........hhhhhhhhhhhhhhhhhhhhhh......eeeeeehhh.eee..hhhhhee...hhhhhhhhhhhhhhhh..eeee.hhhhhhhhh....hhhhhh.......eee..eee.hhhhhhhhhhhhhhhhh......eeeeee..........hhhhhhhhhhhhhhhh.............eee..........hhhhhh................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hpg C   1 xVGVCYGMQGNNLPPVSEVIALYKKSNITRMRIYDPNQAVLEALRGSNIELILGVPNSDLQSLTNPSNAKSWVQKNVRGFWSSVRFRYIAVGNEISPVNRGTAWLAQFVLPAMRNIHDAIRSAGLQDQIKVSTAIDLTLVGNSYPPSAGAFRDDVRSYLNPIIRFLSSIRSPLLANIYPYFTYAGNPRDISLPYALFTSPSVVVWDGQRGYKNLFDATLDALYSALERASGGSLEVVVSESGWPSAGAFAATFDNGRTYLSNLIQHVKRGTPKRPKRAIETYLFAMFDENKKQPEVEKHFGLFFPNKWQKYNLNFS 316
                            |       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      
                            1-PCA

Chain D from PDB  Type:PROTEIN  Length:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4hpgd_ D: automated matches                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.........hhhhhhhhhhhhh..eeee...hhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhhhhh........eeeeeeee........hhhhhhhhhhhhhhhhhhhhhh......eeeeeehhh.eee..hhhhhee...hhhhhhhhhhhhhhh...eeee.hhhhhhhhh....hhhhhhh......eee..eee.hhhhhhhhhhhhhhhh.......eeeeee..........hhhhhhhhhhhhhhhh.............eee..........hhhhhh................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hpg D   1 xVGVCYGMQGNNLPPVSEVIALYKKSNITRMRIYDPNQAVLEALRGSNIELILGVPNSDLQSLTNPSNAKSWVQKNVRGFWSSVRFRYIAVGNEISPVNRGTAWLAQFVLPAMRNIHDAIRSAGLQDQIKVSTAIDLTLVGNSYPPSAGAFRDDVRSYLNPIIRFLSSIRSPLLANIYPYFTYAGNPRDISLPYALFTSPSVVVWDGQRGYKNLFDATLDALYSALERASGGSLEVVVSESGWPSAGAFAATFDNGRTYLSNLIQHVKRGTPKRPKRAIETYLFAMFDENKKQPEVEKHFGLFFPNKWQKYNLNFS 316
                            |       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      
                            1-PCA

Legend:		→ Mismatch	(orange background)
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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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: (Trans)glycosidases (1191)

Family: beta-glycanases (284)

Protein domain: automated matches (49)

Rubber tree (Hevea brasiliensis) [TaxId: 3981] (2)

1a	d4hpga_	A:
1b	d4hpgb_	B:
1c	d4hpgc_	C:
1d	d4hpgd_	D:

(no "CATH Domain" information available for 4HPG, only for superseded entry 3EM5 replaced by 4HPG)

(no "Pfam Domain" information available for 4HPG)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Gln A:293 - Pro A:294	[ RasMol ]
		Gln B:293 - Pro B:294	[ RasMol ]
		Gln C:293 - Pro C:294	[ RasMol ]
		Gln D:293 - Pro D:294	[ RasMol ]
		Phe A:284 - Ala A:285	[ RasMol ]
		Phe B:284 - Ala B:285	[ RasMol ]
		Phe C:284 - Ala C:285	[ RasMol ]
		Phe D:284 - Ala D:285	[ RasMol ]
		Tyr A:144 - Pro A:145	[ RasMol ]
		Tyr B:144 - Pro B:145	[ RasMol ]
		Tyr C:144 - Pro C:145	[ RasMol ]
		Tyr D:144 - Pro D:145	[ RasMol ]

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	4hpg
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 11)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (12, 12)

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