5I04 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE ORPHAN REGION OF HUMAN ENDOGLIN/CD105

Authors :   T. Saito, M. Bokhove, D. De Sanctis, L. Jovine

Date :   03 Feb 16 (Deposition) - 07 Jun 17 (Release) - 14 Jun 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.42

Chains :   Asym./Biol. Unit : A

Keywords :   Orphan Domain, Angiogenesis, Glycoprotein, Receptor, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Saito, M. Bokhove, R. Croci, S. Zamora-Caballero, L. Han, M. Letarte, D. De Sanctis, L. Jovine
Structural Basis Of The Human Endoglin-Bmp9 Interaction: Insights Into Bmp Signaling And Hht1.
Cell Rep V. 19 1917 2017
PubMed-ID: 28564608 | Reference-DOI: 10.1016/J.CELREP.2017.05.011
(for further references see the PDB file header)

Molecule 1 - MALTOSE-BINDING PERIPLASMIC PROTEIN,ENDOGLIN
	Cell	:	ENDOTHELIAL
	Chains	:	A
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Atcc Number	:	CRL-3022
	Expression System Cell Line	:	HEK293S
	Expression System Common	:	HUMAN, HUMAN
	Expression System Plasmid	:	PHLSEC
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Gene	:	MALE, B4034, JW3994, ENG, END
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	ESCHERICHIA COLI K-12, HOMO SAPIENS
	Organism Taxid	:	83333, 9606
	Other Details	:	THIS PROTEIN IS A CHIMERA. RESIDUES 56-422 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 27-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A AND R422N (CORRESPONDING TO I28T, D108A, K109A, E198A, N199A, A241H, K245H, K265A, A338V, I343V, E385A, E388A, D389A AND R393N IN P0AEX9). RESIDUES 426-737 ARE FROM HUMAN ENDOGLIN PROTEIN AND CORRESPOND TO RESIDUES 26-337 OF SWISS-PROT DATABASE ENTRY P17813. SUBTRACTING 400 FROM THE PDB ENTRY RESIDUE NUMBERING RESULTS IN THE NUMBERING ACCORDING TO UNIPROT ENTRY P17813.
	Synonym	:	MBP,MMBP,MALTODEXTRIN-BINDING PROTEIN

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	MAL	1	Ligand/Ion	MALTOSE
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	PGE	3	Ligand/Ion	TRIETHYLENE GLYCOL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:58 , LYS A:61 , GLU A:470 , PHE A:471 , ASN A:502	binding site for residue NAG A 801
2	AC2	SOFTWARE	ASN A:67 , ASP A:69 , LYS A:70 , TRP A:117 , ALA A:118 , ASP A:120 , ARG A:121 , GLU A:166 , GLU A:208 , PRO A:209 , TYR A:210 , PHE A:211 , MET A:385	binding site for residue MAL A 802
3	AC3	SOFTWARE	LYS A:84 , GLU A:479 , SER A:567 , LEU A:569 , GLU A:595 , ILE A:722	binding site for residue PGE A 803
4	AC4	SOFTWARE	THR A:536 , TRP A:549 , ARG A:553	binding site for residue PGE A 804
5	AC5	SOFTWARE	TYR A:145 , PHE A:147 , GLU A:548 , PRO A:555 , ILE A:556	binding site for residue PGE A 805

Asymmetric/Biological Unit

No.	Residues
1	A:430	-	A:607
2	A:453	-	A:582

(no "Cis Peptide Bond" information available for 5I04)

(no "SAP(SNP)/Variant" information available for 5I04)

(no "PROSITE Motif" information available for 5I04)

(no "Exon" information available for 5I04)

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:668
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....hhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhh......eeeee..hhhhhhhh........hhhhhh..hhhhhhhhee..ee..eeeeee..eeeee............hhhhhhhhhhhh..eee.....hhhhhhhhhhhh..eeeeee..eeeeeeee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..eeeeeehhhhhhhhhhh...eeee...ee..ee...eeeeeeeee.....hhhhhhhhhhhh..hhhhhhhhhhhh...ee.hhhhhhhhh.hhhhhhhhhhhhhhee.....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.........ee.....eeeeeee.eeeeeee.......eeeeeeeee.....eeeeeeee......eeeeeeee...eeeeeee....eeeee....eee.......eee....hhhhhhhhhhh...eeeeeeee.eeeeeee.............eeeee....eeeee......eeee........eeeeeeee....eeeeeeeee........eeeeee....eeeeeee....eeee..eeee.......ee......hhhhhhhhhhhh...eeeeeeeee.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i04 A  54 GTKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEHAFNHGETAMTINGPWAWSNIDTSAVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELVKDPRVAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALAAAQTNAAAETVHCDLQPVGPERGEVTYTTSQVSKGCVAQAPNAILEVHVLFLEFPTGPSQLELTLQASKQPREVLLVLSVNSSVFLHLQALGIPLHLAYNSSLVTFQEPPGVNTTELPSFPKTQILEWAAERGPITSAAELNDPQSILLRLGQAQGSLSFCMLEASQDMGRTLEWRPRTPALVRGCHLEGVAGHKEAHILRVLPAGPRTVTVKVELSCAPGDLDAVLILQGPPYVSWLIDANHNMQIWTTGEYSFKIFPEKNIRGFKLPDTPQGLLGEARMLNASIVASFVELPLASIVSLHAS 728
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483   ||  497       507       517       527       537       547       557       567       577       587       597       607       617       630       640       650       660       670       680       690       700       710       720        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                           487|                                                                                                                                  625|                                                                                                   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                            492                                                                                                                                   629

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

(no "SCOP Domain" information available for 5I04)

(no "CATH Domain" information available for 5I04)

(no "Pfam Domain" information available for 5I04)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5i04)

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	MALE_ECOLI \| P0AEX9
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5hzv	CRYSTAL STRUCTURE OF THE ZONA PELLUCIDA MODULE OF HUMAN ENDOGLIN/ CD105
5hzw	CRYSTAL STRUCTURE OF THE ORPHAN REGION OF HUMAN ENDOGLIN/CD105 IN COMPLEX WITH BMP9
5i05	CRYSTAL STRUCTURE OF HUMAN BMP9 AT 1.87 A RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (0, 0)

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Gene Ontology (76, 78)

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