3KH2 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE P1 BACTERIOPHAGE DOC TOXIN (F68S) IN COMPLEX WITH THE PHD ANTITOXIN (L17M/V39A). NORTHEAST STRUCTURAL GENOMICS TARGETS ER385-ER386

Authors :   M. A. Arbing, A. P. Kuzin, M. Su, M. Abashidze, G. Verdon, M. Liu, R. Xiao, M. Inouye, G. T. Montelione, N. A. Woychik, J. F. Hunt, Northeast Stru Genomics Consortium (Nesg)

Date :   29 Oct 09 (Deposition) - 18 Aug 10 (Release) - 18 Aug 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.71

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,E,F  (1x)
Biol. Unit 2: C,D,G,H  (1x)

Keywords :   Toxin, Antitoxin, Structural Genomics, Psi-2, Northeast Structural Genomics Consortium (Nesg), Protein Structure Initiative (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Arbing, S. K. Handelman, A. P. Kuzin, G. Verdon, C. Wang, M. Su, F. P. Rothenbacher, M. Abashidze, M. Liu, J. M. Hurley, R. Xiao, T. Acton, M. Inouye, G. T. Montelione, N. A. Woychik, J. F. Hunt
Crystal Structures Of Phd-Doc, Higa, And Yeeu Establish Multiple Evolutionary Links Between Microbial Growth-Regulating Toxin-Antitoxin Systems.
Structure V. 18 996 2010
PubMed-ID: 20696400 | Reference-DOI: 10.1016/J.STR.2010.04.018

Molecule 1 - DEATH ON CURING PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21C
	Expression System Strain	:	BL21(DE3)+ MAGIC
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	DOC
	Mutation	:	YES
	Organism Scientific	:	BACTERIOPHAGE P1
	Organism Taxid	:	10678

Molecule 2 - PREVENT HOST DEATH PROTEIN
	Chains	:	E, F, G, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21C
	Expression System Strain	:	BL21(DE3)+ MAGIC
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PHD
	Mutation	:	YES
	Organism Scientific	:	BACTERIOPHAGE P1
	Organism Taxid	:	10678

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B			E	F
Biological Unit 2 (1x)	:			C	D			G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 22)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	GOL	3	Ligand/Ion	GLYCEROL
3	HED	2	Ligand/Ion	2-HYDROXYETHYL DISULFIDE
4	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
5	PO4	4	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (4, 12)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	HED	2	Ligand/Ion	2-HYDROXYETHYL DISULFIDE
4	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
5	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (3, 9)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	HED	-1	Ligand/Ion	2-HYDROXYETHYL DISULFIDE
4	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
5	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:71 , LYS A:73 , ARG A:74	BINDING SITE FOR RESIDUE CL A 1001
2	AC2	SOFTWARE	TYR B:45 , ARG C:64 , GLU D:47	BINDING SITE FOR RESIDUE GOL B 2001
3	AC3	SOFTWARE	ARG A:42 , TYR A:45 , GLU A:46 , ARG D:38 , ARG D:42	BINDING SITE FOR RESIDUE HED A 1002
4	AC4	SOFTWARE	ARG B:38 , ARG B:42 , VAL B:111 , ARG C:38 , ARG C:42	BINDING SITE FOR RESIDUE HED B 1001
5	AC5	SOFTWARE	GLN E:2 , GLU E:25 , VAL E:26 , GLU E:27 , VAL E:37	BINDING SITE FOR RESIDUE PO4 E 4003
6	AC6	SOFTWARE	GLN F:2 , GLU F:25 , VAL F:26 , GLU F:27 , VAL F:37	BINDING SITE FOR RESIDUE PO4 F 4001
7	AC7	SOFTWARE	GLN G:2 , GLU G:25 , VAL G:26 , GLU G:27 , GLU H:45	BINDING SITE FOR RESIDUE PO4 G 4002
8	AC8	SOFTWARE	ASP H:53	BINDING SITE FOR RESIDUE GOL H 2003
9	AC9	SOFTWARE	GLN H:2 , GLU H:25 , VAL H:26 , GLU H:27	BINDING SITE FOR RESIDUE PO4 H 4004

(no "SS Bond" information available for 3KH2)

(no "Cis Peptide Bond" information available for 3KH2)

(no "SAP(SNP)/Variant" information available for 3KH2)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FIDO	PS51459	Fido domain profile.	DOC_BPP1	4-120	4	A:4-120 B:4-120 C:4-120 D:4-120

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FIDO	PS51459	Fido domain profile.	DOC_BPP1	4-120	2	A:4-120 B:4-120 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FIDO	PS51459	Fido domain profile.	DOC_BPP1	4-120	2	- - C:4-120 D:4-120

(no "Exon" information available for 3KH2)

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:124
 aligned with DOC_BPP1 | Q06259 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:124
                                    10        20        30        40        50        60        70        80        90       100       110       120    
             DOC_BPP1     1 MRHISPEELIALHDANISRYGGLPGMSDPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGHIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYGS 124
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh........hhhhhhhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---FIDO  PDB: A:4-120 UniProt: 4-120                                                                                    ---- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kh2 A   1 mRHISPEELIALHDANISRYGGLPGmSDPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGHISNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYGS 124
                            |       10        20     |  30        40        50        60        70        80        90       100       110       120    
                            |                       26-MSE                                                                                              
                            1-MSE

Chain B from PDB  Type:PROTEIN  Length:124
 aligned with DOC_BPP1 | Q06259 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:124
                                    10        20        30        40        50        60        70        80        90       100       110       120    
             DOC_BPP1     1 MRHISPEELIALHDANISRYGGLPGMSDPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGHIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYGS 124
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh........hhhhhhhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---FIDO  PDB: B:4-120 UniProt: 4-120                                                                                    ---- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kh2 B   1 mRHISPEELIALHDANISRYGGLPGmSDPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGHISNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYGS 124
                            |       10        20     |  30        40        50        60        70        80        90       100       110       120    
                            1-MSE                   26-MSE

Chain C from PDB  Type:PROTEIN  Length:123
 aligned with DOC_BPP1 | Q06259 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:123
                                    10        20        30        40        50        60        70        80        90       100       110       120   
             DOC_BPP1     1 MRHISPEELIALHDANISRYGGLPGMSDPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGHIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYG 123
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh........hhhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---FIDO  PDB: C:4-120 UniProt: 4-120                                                                                    --- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kh2 C   1 mRHISPEELIALHDANISRYGGLPGmSDPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGHISNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYG 123
                            |       10        20     |  30        40        50        60        70        80        90       100       110       120   
                            1-MSE                   26-MSE

Chain D from PDB  Type:PROTEIN  Length:123
 aligned with DOC_BPP1 | Q06259 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:123
                                    10        20        30        40        50        60        70        80        90       100       110       120   
             DOC_BPP1     1 MRHISPEELIALHDANISRYGGLPGMSDPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGHIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYG 123
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Fic-3kh2D01 D:3-84                                                                --------------------------------------- Pfam domains (1)
           Pfam domains (2) --Fic-3kh2D02 D:3-84                                                                --------------------------------------- Pfam domains (2)
           Pfam domains (3) --Fic-3kh2D03 D:3-84                                                                --------------------------------------- Pfam domains (3)
           Pfam domains (4) --Fic-3kh2D04 D:3-84                                                                --------------------------------------- Pfam domains (4)
         Sec.struct. author ....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh........hhhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---FIDO  PDB: D:4-120 UniProt: 4-120                                                                                    --- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kh2 D   1 mRHISPEELIALHDANISRYGGLPGmSDPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGHISNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYG 123
                            |       10        20     |  30        40        50        60        70        80        90       100       110       120   
                            1-MSE                   26-MSE

Chain E from PDB  Type:PROTEIN  Length:72
 aligned with PHD_BPP1 | Q06253 from UniProtKB/Swiss-Prot  Length:73

    Alignment length:72
                                    11        21        31        41        51        61        71  
             PHD_BPP1     2 QSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDAEFASLFDTLDSTNKELVNR  73
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhhhh..eeee......eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 3kh2 E   2 QSINFRTARGNLSEVmNNVEAGEEVEITRRGREPAVIASKATFEAYKKAALDAEFASLFDTLDSTNKELVNR  73
                                    11     |  21        31        41        51        61        71  
                                          17-MSE

Chain F from PDB  Type:PROTEIN  Length:72
 aligned with PHD_BPP1 | Q06253 from UniProtKB/Swiss-Prot  Length:73

    Alignment length:72
                                    11        21        31        41        51        61        71  
             PHD_BPP1     2 QSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDAEFASLFDTLDSTNKELVNR  73
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhhhh..eeee......eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 3kh2 F   2 QSINFRTARGNLSEVmNNVEAGEEVEITRRGREPAVIASKATFEAYKKAALDAEFASLFDTLDSTNKELVNR  73
                                    11     |  21        31        41        51        61        71  
                                          17-MSE

Chain G from PDB  Type:PROTEIN  Length:72
 aligned with PHD_BPP1 | Q06253 from UniProtKB/Swiss-Prot  Length:73

    Alignment length:72
                                    11        21        31        41        51        61        71  
             PHD_BPP1     2 QSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDAEFASLFDTLDSTNKELVNR  73
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhhhh..eeee......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 3kh2 G   2 QSINFRTARGNLSEVmNNVEAGEEVEITRRGREPAVIASKATFEAYKKAALDAEFASLFDTLDSTNKELVNR  73
                                    11     |  21        31        41        51        61        71  
                                          17-MSE

Chain H from PDB  Type:PROTEIN  Length:72
 aligned with PHD_BPP1 | Q06253 from UniProtKB/Swiss-Prot  Length:73

    Alignment length:72
                                    11        21        31        41        51        61        71  
             PHD_BPP1     2 QSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDAEFASLFDTLDSTNKELVNR  73
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
           Pfam domains (1) PhdYeFM_antitox-3kh2H01 H:2-73                                           Pfam domains (1)
           Pfam domains (2) PhdYeFM_antitox-3kh2H02 H:2-73                                           Pfam domains (2)
           Pfam domains (3) PhdYeFM_antitox-3kh2H03 H:2-73                                           Pfam domains (3)
           Pfam domains (4) PhdYeFM_antitox-3kh2H04 H:2-73                                           Pfam domains (4)
         Sec.struct. author .eeehhhhhhhhhhhhhhhhhh..eeee......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 3kh2 H   2 QSINFRTARGNLSEVmNNVEAGEEVEITRRGREPAVIASKATFEAYKKAALDAEFASLFDTLDSTNKELVNR  73
                                    11     |  21        31        41        51        61        71  
                                          17-MSE

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 '\|'

(no "SCOP Domain" information available for 3KH2)

(no "CATH Domain" information available for 3KH2)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DOC_BPP1 | Q06259)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004674	protein serine/threonine kinase activity	Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006417	regulation of translation	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0039604	suppression by virus of host translation	Any process in which a virus prevents or reduces the frequency, rate or extent of translation of host mRNA.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

Chain E,F,G,H (PHD_BPP1 | Q06253)

molecular function
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

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(no "Cis Peptide Bonds" information available for 3kh2)

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	3kh2
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UniProtKB/Swiss-Prot
	DOC_BPP1 \| Q06259	:	3dd7 3dd9 3k33
	PHD_BPP1 \| Q06253	:	3dd7 3hry 3hs2 3k33 4zlx 4zm0 4zm2

(no "Related Entries Specified in the PDB File" available for 3KH2)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 22)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

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Pfam Domains (2, 8)

Gene Ontology (13, 16)

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Related Entries Specified in the PDB File