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(-) Description

Title :  X-RAY STRUCTURE OF NEUROPILIN-1 B1 DOMAIN COMPLEXED WITH ARG-6 LIGAND.
 
Authors :  C. Fotinou, R. Rana, S. Djordjevic, T. Yelland
Date :  21 Apr 16  (Deposition) - 24 May 17  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Signaling Protein, Neuropilin-1, Angiogenesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Fotinou, R. Rana, S. Djordjevic, T. Yelland
X-Ray Structure Of Neuropilin-1 B1 Domain Complexed With Arg-6 Ligand.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NEUROPILIN-1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B-TEV-NRP1B1
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA-GAMI2-PLYSS
    Expression System Vector: PET15B-TEV
    Expression System Vector Type: PLASMID
    Gene: NRP1, NRP, VEGF165R
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: VASCULAR ENDOTHELIAL CELL GROWTH FACTOR 165 RECEPTOR

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
16K81Ligand/IonN-(BENZENECARBONYL)GLYCYL-L-ARGININE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
16K81Ligand/IonN-(BENZENECARBONYL)GLYCYL-L-ARGININE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
16K8-1Ligand/IonN-(BENZENECARBONYL)GLYCYL-L-ARGININE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:297 , TRP A:301 , THR A:316 , ASP A:320 , SER A:346 , THR A:349 , TYR A:353 , GLY A:414 , ILE A:415 , HOH A:606 , HOH A:632 , HOH A:677 , MET B:276 , TYR B:422binding site for residue 6K8 A 501

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:275 -A:424
2B:275 -B:424

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JHK)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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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:154
                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhh.eee....hhhhhhhhhh..................eeee....eeeeeeeee...........eeeeeeeeee...........................eeee....eee.eeeeee.eee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jhk A 274 KCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVDLGLLRFVTAVGTQGAISKETKKKYYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTDVVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKIT 427
                                   283       293       303       313       323       333       343       353       363       373       383       393       403       413       423    


Chain B from PDB  Type:PROTEIN  Length:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhh.eee....hhhhhhhhhh..................eeee....eeeeeeeee...........eeeeeeeeee...........................eeee....eee.eeeeee.eee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jhk B 270 GHMFKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVDLGLLRFVTAVGTQGAISKETKKKYYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTDVVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKIT 427
                                   279       289       299       309       319       329       339       349       359       369       379       389       399       409       419
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  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 5JHK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (104, 104)

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 Related Entries

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UniProtKB/Swiss-Prot
        NRP1_HUMAN | O14786: 1kex 2qqi 2qqm 2qqn 3i97 4deq 4rn5 5c7g 5ijr 5iyy 5j1x 5jgi 5jgq 5l73

(-) Related Entries Specified in the PDB File

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