Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  COMPLEX OF NOTCH1 (EGF11-13) BOUND TO DELTA-LIKE 4 (N-EGF1)
 
Authors :  V. C. Luca, K. M. Jude, K. C. Garcia
Date :  13 Jan 15  (Deposition) - 04 Mar 15  (Release) - 11 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  D,E  (1x)
Biol. Unit 3:  A,B,D,E  (1x)
Keywords :  Glycosylation, Egf Domains, Receptor-Ligand Complex, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. C. Luca, K. M. Jude, N. W. Pierce, M. V. Nachury, S. Fischer, K. C. Garcia
Structural Biology. Structural Basis For Notch1 Engagement Of Delta-Like 4.
Science V. 347 847 2015
PubMed-ID: 25700513  |  Reference-DOI: 10.1126/SCIENCE.1261093

(-) Compounds

Molecule 1 - NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1
    Chains: A, D
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HI-FIVE
    Expression System Plasmid: PACGP67A
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Gene: NOTCH1
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: NOTCH 1
 
Molecule 2 - DELTA-LIKE PROTEIN
    Chains: B, E
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HI-FIVE
    Expression System Plasmid: PACGP67A
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Gene: DLL4, DLL4_PREDICTED, RCG_26804
    Mutation: YES
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Other Details: METHYLATED IN VITRO

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABDE
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   DE
Biological Unit 3 (1x): ABDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 34)

Asymmetric Unit (5, 34)
No.NameCountTypeFull Name
1BGC6Ligand/IonBETA-D-GLUCOSE
2CA6Ligand/IonCALCIUM ION
3FUC2Ligand/IonALPHA-L-FUCOSE
4MLY12Mod. Amino AcidN-DIMETHYL-LYSINE
5NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (4, 14)
No.NameCountTypeFull Name
1BGC3Ligand/IonBETA-D-GLUCOSE
2CA-1Ligand/IonCALCIUM ION
3FUC1Ligand/IonALPHA-L-FUCOSE
4MLY6Mod. Amino AcidN-DIMETHYL-LYSINE
5NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (4, 14)
No.NameCountTypeFull Name
1BGC3Ligand/IonBETA-D-GLUCOSE
2CA-1Ligand/IonCALCIUM ION
3FUC1Ligand/IonALPHA-L-FUCOSE
4MLY6Mod. Amino AcidN-DIMETHYL-LYSINE
5NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 3 (4, 28)
No.NameCountTypeFull Name
1BGC6Ligand/IonBETA-D-GLUCOSE
2CA-1Ligand/IonCALCIUM ION
3FUC2Ligand/IonALPHA-L-FUCOSE
4MLY12Mod. Amino AcidN-DIMETHYL-LYSINE
5NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:415 , SER A:435 , PHE A:436 , HOH A:714 , HOH A:734 , ASP B:218 , GLU E:51binding site for residue BGC A 601
02AC2SOFTWAREASP A:452 , VAL A:453 , GLU A:455 , ASP A:469 , GLN A:470 , HOH A:729 , HOH A:740binding site for residue CA A 605
03AC3SOFTWAREASN A:490 , THR A:491 , GLU A:493 , ASP A:507 , LYS A:508 , HOH A:702 , HOH A:727binding site for residue CA A 606
04AC4SOFTWAREGLU A:415 , ASN A:431 , THR A:432 , LEU A:433 , GLY A:434 , SER A:435 , HOH A:773binding site for residue CA A 607
05AC5SOFTWAREASN D:490 , THR D:491 , GLU D:493 , ASP D:507 , LYS D:508 , HOH D:717binding site for residue CA D 605
06AC6SOFTWAREASP D:452 , VAL D:453 , GLU D:455 , ASP D:469 , GLN D:470 , HOH D:715 , HOH D:718binding site for residue CA D 606
07AC7SOFTWAREASP D:412 , VAL D:413 , GLU D:415 , ASN D:431 , THR D:432 , LEU D:433 , GLY D:434 , SER D:435binding site for residue CA D 607
08AC8SOFTWAREGLU A:455 , SER A:458 , PHE A:474 , HOH A:741binding site for Mono-Saccharide BGC A 602 bound to SER A 458
09AC9SOFTWAREASP A:464 , THR A:466 , ILE A:477 , HOH A:717 , HOH A:718 , HOH A:726 , HOH A:755 , HIS B:64 , TYR B:65 , THR B:114binding site for Mono-Saccharide FUC A 603 bound to THR A 466
10AD1SOFTWAREGLU A:493 , SER A:496binding site for Mono-Saccharide BGC A 604 bound to SER A 496
11AD2SOFTWAREPRO B:73 , CYS B:74 , ASN B:78 , HOH B:439 , GLU D:511binding site for Mono-Saccharide NAG B 301 bound to ASN B 78
12AD3SOFTWAREILE A:471 , ASN B:108 , SER D:527binding site for Mono-Saccharide NAG B 302 bound to ASN B 108
13AD4SOFTWAREGLU B:159 , ASN B:161 , HOH B:456 , ASN E:161 , ASN E:162binding site for Poly-Saccharide residues NAG B 303 through NAG B 304 bound to ASN B 161
14AD5SOFTWARESER D:435 , PHE D:436 , HOH D:729 , ASP E:218 , GLN E:219binding site for Mono-Saccharide BGC D 601 bound to SER D 435
15AD6SOFTWAREGLU D:455 , SER D:458 , PHE D:474 , PRO E:135binding site for Mono-Saccharide BGC D 602 bound to SER D 458
16AD7SOFTWAREASP D:464 , THR D:466 , ILE D:477 , HIS E:64 , TYR E:65binding site for Mono-Saccharide FUC D 603 bound to THR D 466
17AD8SOFTWAREGLU D:493 , SER D:496binding site for Mono-Saccharide BGC D 604 bound to SER D 496
18AD9SOFTWAREGLU A:511 , CYS E:74 , ASN E:78 , HOH E:446binding site for Mono-Saccharide NAG E 301 bound to ASN E 78
19AE1SOFTWAREGLY E:25 , ASN E:108binding site for Mono-Saccharide NAG E 302 bound to ASN E 108
20AE2SOFTWAREASN B:161 , ASN B:162 , ALA D:417 , GLY D:419 , GLU E:159 , ASN E:161 , ARG E:166 , HOH E:463binding site for Poly-Saccharide residues NAG E 303 through NAG E 304 bound to ASN E 161

(-) SS Bonds  (34, 34)

Asymmetric Unit
No.Residues
1A:416 -A:429
2A:423 -A:438
3A:440 -A:449
4A:456 -A:467
5A:461 -A:476
6A:478 -A:487
7A:494 -A:505
8A:499 -A:514
9A:516 -A:525
10B:50 -B:54
11B:61 -B:74
12B:175 -B:184
13B:188 -B:200
14B:208 -B:217
15B:222 -B:233
16B:226 -B:239
17B:241 -B:250
18D:416 -D:429
19D:423 -D:438
20D:440 -D:449
21D:456 -D:467
22D:461 -D:476
23D:478 -D:487
24D:494 -D:505
25D:499 -D:514
26D:516 -D:525
27E:50 -E:54
28E:61 -E:74
29E:175 -E:184
30E:188 -E:200
31E:208 -E:217
32E:222 -E:233
33E:226 -E:239
34E:241 -E:250

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu B:51 -Pro B:52
2Asn B:101 -Pro B:102
3Glu E:51 -Pro E:52
4Asn E:101 -Pro E:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XL1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XL1)

(-) Exons   (0, 0)

(no "Exon" information available for 4XL1)

(-) 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:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh........eeeee..eeeee....ee.....ee.............eeeee..eeeee....ee.....ee.............eeee....eeee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 4xl1 A 414 DECALGANPCEHAGKCLNTLGSFECQCLQGYTGPRCEIDVNECISNPCQNDATCLDQIGEFQCICMPGYEGVYCEINTDECASSPCLHNGRCVDKINEFLCQCPKGFSGHLCQSG 528
                                   423       433       443       453       463       473       483       493       503       513       523     


Chain B from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee................eeeeeeeee.............eeee....ee..ee..........eeeee......eeeeeeeeee......hhhhh...eeeeeeeeeee.......eeeeeee...eeeeeeeeee...ee.....ee...eee..eeeee.....eee...ee.....ee..........ee.......ee...ee.....ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xl1 B  26 SSSIFQLRLQEFANERGMLANGRPCEPGCRTFFRICLkHYQATFSEGPCTFGNVSTPVLGTNSFVIRDKNSGRNPLQLPLNFTWPGTFSLNIQAWHTPGDDLRPETSPGNSLISQIIIQGSLAVGkNWKSDEQNNTLTRLRYSYRVVCSDNYYGDSCSRLCkkRDDHFGHYECQPDGSPSCLPGWTGkYCDQPICLSGCHEQNGYCSkPDECNCRPGWQGPLCNEAA 254
                                    35        45        55       |65        75        85        95||     107       117       127       137       147     | 157       167       177       187 ||    197       207       217       227       237       247       
                                                                63-MLY                           96|                                                   153-MLY                             189-MLY                   215-MLY             235-MLY               
                                                                                                  99                                                                                        190-MLY                                                            


Chain D from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeee..eeeee....ee.....ee.............eeeee..eeeee....ee.....ee.............eeee....eeee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 4xl1 D 411 PDVDECALGANPCEHAGKCLNTLGSFECQCLQGYTGPRCEIDVNECISNPCQNDATCLDQIGEFQCICMPGYEGVYCEINTDECASSPCLHNGRCVDKINEFLCQCPKGFSGHLCQS 527
                                   420       430       440       450       460       470       480       490       500       510       520       


Chain E from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeee................eeeeeeeee.............eeee....ee..ee............eeeee......eeeeeeeeee......hhhhh...eeeeeeeeeee.......eeeeeee...eeeeeeeeee...ee.....ee...eee..eeeee.....eee...ee.....ee..........ee.......ee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xl1 E  25 GSSSIFQLRLQEFANERGMLANGRPCEPGCRTFFRICLkHYQATFSEGPCTFGNVSTPVLGTNSFVIRDKNSGSGRNPLQLPLNFTWPGTFSLNIQAWHTPGDDLRPETSPGNSLISQIIIQGSLAVGkNWKSDEQNNTLTRLRYSYRVVCSDNYYGDSCSRLCkkRDDHFGHYECQPDGSPSCLPGWTGkYCDQPICLSGCHEQNGYCSkPDECNCRPGWQGPLCNEA 253
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184    || 194       204       214|      224       234|      244         
                                                                 63-MLY                                                                                   153-MLY                             189-MLY                   215-MLY             235-MLY              
                                                                                                                                                                                               190-MLY
   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 4XL1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XL1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XL1)

(-) Gene Ontology  (202, 221)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BGC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FUC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MLY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
    AD6  [ RasMol ]  +environment [ RasMol ]
    AD7  [ RasMol ]  +environment [ RasMol ]
    AD8  [ RasMol ]  +environment [ RasMol ]
    AD9  [ RasMol ]  +environment [ RasMol ]
    AE1  [ RasMol ]  +environment [ RasMol ]
    AE2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn B:101 - Pro B:102   [ RasMol ]  
    Asn E:101 - Pro E:102   [ RasMol ]  
    Glu B:51 - Pro B:52   [ RasMol ]  
    Glu E:51 - Pro E:52   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4xl1
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DLL4_RAT | D3ZHH1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  NOTC1_RAT | Q07008
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  DLL4_RAT | D3ZHH1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  NOTC1_RAT | Q07008
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DLL4_RAT | D3ZHH1: 4xlw
        NOTC1_RAT | Q07008: 1ymp 4xlw 5uk5

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4XL1)