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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ORPHAN REGION OF HUMAN ENDOGLIN/CD105 IN COMPLEX WITH BMP9
 
Authors :  M. Bokhove, T. Saito, L. Jovine
Date :  03 Feb 16  (Deposition) - 07 Jun 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
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)

(-) Compounds

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
    Expression System Plasmid: PHLSEC
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 27-393,UNP RESIDUES 25-337,UNP RESIDUES 27- 393,UNP RESIDUES 25-337
    Gene: MALE, B4034, JW3994, ENG, END
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: ESCHERICHIA COLI K12, 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
 
Molecule 2 - GROWTH/DIFFERENTIATION FACTOR 2
    Chains: B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Atcc Number: CRL-3022
    Expression System Cell Line: HEK293S
    Expression System Common: HUMAN
    Expression System Plasmid: PHLSEC
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 320-429
    Gene: GDF2, BMP9
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: MATURE BMP9
    Synonym: GDF-2,BONE MORPHOGENETIC PROTEIN 9,BMP-9

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1MAL1Ligand/IonMALTOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1MAL2Ligand/IonMALTOSE
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS 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:210binding site for residue MAL A 803
2AC2SOFTWAREGLU A:59 , GLY A:60 , LYS A:61 , PRO A:326 , ASN A:327 , PHE A:471 , THR A:473 , ASN A:502binding site for Mono-Saccharide NAG A 801 bound to ASN A 502
3AC3SOFTWAREASN A:521 , SER A:523 , LEU A:524 , LEU A:538 , PRO A:539 , SER A:540binding site for Mono-Saccharide NAG A 802 bound to ASN A 521

(-) SS Bonds  (7, 7)

Asymmetric Unit
No.Residues
1A:430 -A:607
2A:453 -A:582
3A:642 -A:730
4B:8 -B:74
5B:37 -B:107
6B:41 -B:109
7B:73 -B:73

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala B:28 -Pro B:29
2Phe B:43 -Pro B:44

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HZW)

(-) 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:668
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhhhheeeeee...hhhhhhhhhhh......eeeeehhhhhhhhhh........hhhhhhhhhhhhhhhhee..ee.eeeeeee..eeeee.........hhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhh....eee..eee.......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..eeeeee..hhhhhhhhh...eeee...ee..ee...eeeeeeeee.....hhhhhhhhhhhh..hhhhhhhhhhhh......hhhhhhhhh.hhhhhhhhhhhhhhee.....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........ee.....eeeeeee.eeeeeee.......eeeeeeeee.....eeeeeeee......eeeeeeee...eeeeeee....eeee.....eee..............hhhhhhhhhhh...eeeeeeee.eeeeeee.............eeeee....eeeee......eeee........eeeeeee........eeeeeeeee........eeeeee....eeeeee....eeeee..eeee.......ee......hhhhhhhhhhhh...eeeeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hzw A  59 EGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEHAFNHGETAMTINGPWAWSNIDTSAVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELVKDPRVAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALAAAQTNAAAETVHCDLQPVGPERGEVTYTTSQVSKGCVAQAPNAILEVHVLFLEFPTGPSQLELTLQASKQPREVLLVLSVNSSVFLHLQALGIPLHLAYNSSLVTFQEPPGVNTTELPSFPKTQILEWAAERGPITSAAELNDPQSILLRLGQAQGSLSFCMLEASQDMGRTLEWRPRTPALVRGCHLEGVAGHKEAHILRVLPGHSAGPRTVTVKVELSCAPGDLDAVLILQGPPYVSWLIDANHNMQIWTTGEYSFKIFPEKNIRGFKLPDTPQGLLGEARMLNASIVASFVELPLASIVSLHASSC 730
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                      487|                                                                                                                                                                                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                                                       492                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eee..............eee..eee.............hhhhhhhhhhhhhh........eeeeeeeeeeeeee.....eeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 5hzw B   6 SHCQKTSLRVNFEDIGWDSWIIAPKEYEAYECKGGCFFPLADDVTPTKHAIVQTLVHLKFPTKVGKACCVPTKLSPISVLYKDDMGVPTLKYHYEGMSVAECGCR 110
                                    15        25        35        45        55        65        75        85        95       105
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (108, 121)

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  5hzw
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        EGLN_HUMAN | P17813: 5hzv 5i04
        GDF2_HUMAN | Q9UK05: 1zkz 4fao 4mpl 4ycg 4yci 5i05
        MALE_ECOLI | P0AEX9: 1a7l 1anf 1dmb 1ez9 1ezo 1ezp 1fqa 1fqb 1fqc 1fqd 1hsj 1iud 1jvx 1jvy 1jw4 1jw5 1lax 1lls 1mdp 1mdq 1mg1 1mh3 1mh4 1mpb 1mpc 1mpd 1n3w 1n3x 1nl5 1nmu 1omp 1peb 1r6z 1svx 1t0k 1y4c 1ytv 1ziu 1zjl 1zkb 1zmg 2d21 2h25 2klf 2mv0 2n44 2n45 2nvu 2obg 2ok2 2r6g 2v93 2vgq 2xz3 2zxt 3a3c 3c4m 3csb 3csg 3d4c 3d4g 3dm0 3ef7 3ehs 3eht 3ehu 3f5f 3g7v 3g7w 3h3g 3h4z 3hpi 3hst 3io4 3io6 3ior 3iot 3iou 3iov 3iow 3j9p 3kjt 3l2j 3lbs 3lc8 3mbp 3mp1 3mp6 3mp8 3mq9 3n94 3o3u 3oai 3osq 3osr 3pgf 3puv 3puw 3pux 3puy 3puz 3pv0 3py7 3q25 3q26 3q27 3q28 3q29 3rlf 3rum 3ser 3ses 3set 3seu 3sev 3sew 3sex 3sey 3vfj 3w15 3wai 3woa 4b3n 4bl8 4bl9 4bla 4blb 4bld 4dxb 4dxc 4edq 4egc 4exk 4fe8 4feb 4fec 4fed 4giz 4gli 4ifp 4ikm 4irl 4jbz 4jkm 4keg 4khz 4ki0 4kv3 4kyc 4kyd 4kye 4log 4mbp 4n4x 4ndz 4o2x 4ogm 4pe2 4qsz 4qvh 4r0y 4rg5 4rwf 4rwg 4tsm 4wjv 4wms 4wmt 4wmu 4wmv 4wmw 4wmx 4wrn 4wth 4wvh 4xa2 4xhs 4xr8 4xzs 4xzv 5aq9 5az6 5az7 5az8 5az9 5aza 5b3w 5b3x 5b3y 5b3z 5c7r 5cbn 5cfv 5dfm 5dis 5e24 5edu 5fio 5fsg 5gru 5gs2 5h7n 5h7q 5hz7 5hzv 5i04 5i69 5ihj 5ii5 5iic 5iqz 5jj4 5jst 5jtq 5jtr 5ldf 5t03 5t05 5t0a 5ttd 5wpz 5wq6

(-) Related Entries Specified in the PDB File

5hzv CRYSTAL STRUCTURE OF THE ZONA PELLUCIDA MODULE OF HUMAN ENDOGLIN/ CD105
5i04 CRYSTAL STRUCTURE OF THE ORPHAN REGION OF HUMAN ENDOGLIN/CD105
5i05 CRYSTAL STRUCTURE OF HUMAN BMP9 AT 1.87 A RESOLUTION