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(-) Description

Title :  B1 DOMAIN OF HUMAN NEUROPILIN-1 WITH ACETATE ION IN A LIGAND-BINDING SITE
 
Authors :  C. K. Allerston, T. S. Yelland, A. Jarvis, K. Jenkins, N. Winfield, L. Ch H. Jia, I. Zachary, D. L. Selwood, S. Djordjevic
Date :  23 Oct 14  (Deposition) - 28 Oct 15  (Release) - 28 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  A
Keywords :  Vegf Binding, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. K. Allerston, T. S. Yelland, A. Jarvis, K. Jenkins, N. Winfield, L. Cheng, H. Jia, I. Zachary, D. L. Selwood, S. Djordjevic
Conserved Water Molecules In A Ligand-Binding Site Of Neuropilin-1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NEUROPILIN-1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: B1 DOMAIN (UNP RESIDUES 273-427)
    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

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:301 , SER A:346 , THR A:349 , TYR A:353 , ARG A:402 , HOH A:643BINDING SITE FOR RESIDUE ACT A 501
2AC2SOFTWAREGLY A:270 , HIS A:287 , GLU A:319 , HOH A:685BINDING SITE FOR RESIDUE ZN A 502
3AC3SOFTWAREASP A:289 , ASP A:320 , HOH A:755 , HOH A:756 , HOH A:757 , HOH A:759BINDING SITE FOR RESIDUE ZN A 503
4AC4SOFTWARELEU A:279 , GLU A:285 , GLN A:290 , LEU A:330 , ARG A:334 , HOH A:679 , HOH A:713BINDING SITE FOR RESIDUE GOL A 504

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:275 -A:424

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4RN5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RN5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RN5)

(-) Exons   (0, 0)

(no "Exon" information available for 4RN5)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee........hhh.eee....hhhhhhhhhh..................eeeeeeeeeeeeeeeee.ee......eeeeeeeeeeee.....eee.ee..ee..ee........eeeeeeeeeeeeeeeeeeeeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rn5 A 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 4RN5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RN5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RN5)

(-) Gene Ontology  (104, 104)

Asymmetric/Biological Unit(hide GO term definitions)

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  4rn5
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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 5c7g 5ijr 5iyy 5j1x 5jgi 5jgq 5jhk 5l73

(-) Related Entries Specified in the PDB File

4rn8 4rn9