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(-) Description

Title :  MAM DOMAIN OF HUMAN NEUROPILIN-1
 
Authors :  T. Yelland, S. Djordjevic
Date :  01 Jun 16  (Deposition) - 26 Oct 16  (Release) - 09 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Mam Domain, Dimerisation Domain, Neuropilin, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Yelland, S. Djordjevic
Crystal Structure Of The Neuropilin-1 Mam Domain: Completin The Neuropilin-1 Ectodomain Picture.
Structure V. 24 2008 2016
PubMed-ID: 27720589  |  Reference-DOI: 10.1016/J.STR.2016.08.017

(-) Compounds

Molecule 1 - NEUROPILIN-1
    Chains: A, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 628-813
    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/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1BCN2Ligand/IonBICINE
2CA4Ligand/IonCALCIUM ION
3TAM1Ligand/IonTRIS(HYDROXYETHYL)AMINOMETHANE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:651 , ASP A:685 , ASN A:691 , ASP A:796 , HOH A:1033binding site for residue CA A 901
2AC2SOFTWAREASP A:685 , BCN A:903 , HOH A:1035 , HOH A:1065binding site for residue CA A 902
3AC3SOFTWAREASP A:685 , HIS A:686 , THR A:687 , TRP A:725 , TRP A:763 , ASP A:796 , CA A:902 , HOH A:1027 , HOH A:1035 , HOH A:1065 , GLU B:765 , ARG B:767binding site for residue BCN A 903
4AC4SOFTWAREPRO A:644 , ASP A:645 , GLY A:647 , ASN A:649 , THR A:659 , CYS A:661 , SER A:731 , ILE A:756 , HIS A:758 , GLN A:759 , HOH A:1003 , HOH A:1005binding site for residue TAM A 904
5AC5SOFTWAREGLU B:651 , ASP B:685 , ASN B:691 , ASP B:796 , HOH B:1014binding site for residue CA B 901
6AC6SOFTWAREASP B:685 , THR B:687 , BCN B:903 , HOH B:1019binding site for residue CA B 902
7AC7SOFTWAREASP B:685 , HIS B:686 , THR B:687 , TRP B:725 , TRP B:763 , ASP B:796 , ASP B:797 , CA B:902 , HOH B:1019binding site for residue BCN B 903

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:650 -A:661
2A:721 -A:809
3B:650 -B:661
4B:721 -B:809

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5L73)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L73)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L73)

(-) Exons   (0, 0)

(no "Exon" information available for 5L73)

(-) Sequences/Alignments

Asymmetric/Biological 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:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh......ee..ee.....ee........eeee.............eeeeee.hhhhh..eeeeeeeee......eeeeeeeee.....eeeeeeeee......eeeeeeee.......eeeeeee......eeeeeeeee......eeeeeeeee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5l73 A 640 QDEFPDYGFNCEFGWGSHKTFCHWEHDNHVQLKWSVLTSKTGPIQDHTGDGNFIYSQADENQKGKVARLVSPVVYSQNSAHCMTFWYHMSGSHVGTLRVKLRYQKPEEYDQLVWMAIGHQGDHWKEGRVLLHKSLKLYQVIFEGEIGKGNLGGIAVDDISINNHISQEDCAKPA 813
                                   649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809    


Chain B from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........ee..ee.....ee........eeee.............eeeeee.hhhhh..eeeee..........eeeeeeeee.....eeeeeeeee.....eeeeeeeee.......eeeeeee......eeeeeeeee......eeeeeeee.....hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5l73 B 642 EFPDYGFNCEFGWGSHKTFCHWEHDNHVQLKWSVLTSKTGPIQDHTGDGNFIYSQADENQKGKVARLVSPVVYSQNSAHCMTFWYHMSGSHVGTLRVKLRYQKPEEYDQLVWMAIGHQGDHWKEGRVLLHKSLKLYQVIFEGEIGKGNLGGIAVDDISINNHISQEDCAKPAHH 815
                                   651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811
   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 5L73)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L73)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L73)

(-) Gene Ontology  (104, 104)

Asymmetric/Biological Unit(hide GO term definitions)

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  5l73
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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 5iyy 5j1x 5jgi 5jgq 5jhk

(-) Related Entries Specified in the PDB File

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