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(-) Description

Title :  X-RAY STRUCTURE OF NEUROPILIN-1 B1 DOMAIN COMPLEXED WITH ARG-4 LIGAND.
 
Authors :  C. Fotinou, R. Rana, S. Djordjevic, T. Yelland
Date :  24 Mar 16  (Deposition) - 05 Apr 17  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
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-4 Ligand.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NEUROPILIN-1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    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, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1R402Ligand/IonN~2~-[(BENZYLOXY)CARBONYL]-L-ARGININE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1R401Ligand/IonN~2~-[(BENZYLOXY)CARBONYL]-L-ARGININE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1R401Ligand/IonN~2~-[(BENZYLOXY)CARBONYL]-L-ARGININE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
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:607 , HOH A:626 , HOH A:665 , HOH A:736 , HOH A:757 , MET B:276 , TYR B:422binding site for residue R40 A 501
2AC2SOFTWARETYR B:297 , THR B:316 , ASP B:320 , SER B:346 , THR B:349 , TYR B:353 , GLY B:414 , ILE B:415 , HOH B:655 , HOH B:667 , HOH B:706 , HOH B:716 , HOH B:726binding site for residue R40 B 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 5IYY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IYY)

(-) 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:156
                                                                                                                                                                                            
               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
                 5iyy A 272 MFKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVDLGLLRFVTAVGTQGAISKETKKKYYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTDVVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKIT 427
                                   281       291       301       311       321       331       341       351       361       371       381       391       401       411       421      


Chain B from PDB  Type:PROTEIN  Length:157
                                                                                                                                                                                             
               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
                 5iyy B 271 HMFKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVDLGLLRFVTAVGTQGAISKETKKKYYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTDVVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKIT 427
                                   280       290       300       310       320       330       340       350       360       370       380       390       400       410       420
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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 5IYY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (104, 104)

Asymmetric Unit(hide GO term definitions)

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  5iyy
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  NRP1_HUMAN | O14786
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

5ijr 5IJR CONTAINS THE SAME PROTEIN WITH DIFFERENT ARG-ANALOGUE SMALL MOLECULE