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(-) Description

Title :  NEUROPILIN-2 A1A2B1B2 DOMAINS IN COMPLEX WITH A SEMAPHORIN-BLOCKING FAB
 
Authors :  B. A. Appleton, C. Wiesmann
Date :  26 Jul 07  (Deposition) - 20 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,H,L
Biol. Unit 1:  A (2x),H (2x),L (2x)
Biol. Unit 2:  A,H,L  (1x)
Keywords :  Vegf Receptor, Semaphorin Receptor, Phage-Derived Antibody, Developmental Protein, Differentiation, Glycoprotein, Membrane, Neurogenesis, Transmembrane, Hormone, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. A. Appleton, P. Wu, J. Maloney, J. Yin, W. C. Liang, S. Stawicki, K. Mortara, K. K. Bowman, J. M. Elliott, W. Desmarais, J. F. Bazan, A. Bagri, M. Tessier-Lavigne, A. W. Koch, Y. Wu, R. J. Watts, C. Wiesman
Structural Studies Of Neuropilin/Antibody Complexes Provide Insights Into Semaphorin And Vegf Binding
Embo J. V. 26 4902 2007
PubMed-ID: 17989695  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601906

(-) Compounds

Molecule 1 - NEUROPILIN-2
    ChainsA
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System CommonCABBAGE LOOPER
    Expression System Taxid7111
    Expression System Vector TypeBACULOVIRUS
    FragmentCUB 1, CUB2, F5/8 TYPE C 1, AND C2 DOMAINS
    GeneNRP2, VEGF165R2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymVASCULAR ENDOTHELIAL CELL GROWTH FACTOR 165 RECEPTOR 2
 
Molecule 2 - ANTIBODY HEAVY CHAIN
    ChainsH
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - ANTIBODY LIGHT CHAIN
    ChainsL
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit AHL
Biological Unit 1 (2x)A (2x)H (2x)L (2x)
Biological Unit 2 (1x)AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:150 , ASN A:152BINDING SITE FOR RESIDUE NAG A 1
2AC2SOFTWAREASN A:157BINDING SITE FOR RESIDUE NAG A 602

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:28 -A:55
2A:83 -A:105
3A:149 -A:175
4A:277 -A:427
5A:434 -A:592
6H:22 -H:92
7H:140 -H:196
8L:23 -L:88
9L:134 -L:194

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Tyr A:45 -Pro A:46
2Phe A:165 -Pro A:166
3Phe H:146 -Pro H:147
4Glu H:148 -Pro H:149
5Ser L:7 -Pro L:8
6Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_047754R123KNRP2_HUMANPolymorphism849541AK123K
2UniProtVAR_066403W41RIGKC_HUMANDisease (IGKCD)  ---LW148R
3UniProtVAR_003897V84LIGKC_HUMANPolymorphism  ---LV191L
4UniProtVAR_067537R334CNRP2_HUMANPolymorphism114144673AR334C
5UniProtVAR_067538R428WNRP2_HUMANPolymorphism139711818AR428W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (5, 10)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_047754R123KNRP2_HUMANPolymorphism849541AK123K
2UniProtVAR_066403W41RIGKC_HUMANDisease (IGKCD)  ---LW148R
3UniProtVAR_003897V84LIGKC_HUMANPolymorphism  ---LV191L
4UniProtVAR_067537R334CNRP2_HUMANPolymorphism114144673AR334C
5UniProtVAR_067538R428WNRP2_HUMANPolymorphism139711818AR428W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_047754R123KNRP2_HUMANPolymorphism849541AK123K
2UniProtVAR_066403W41RIGKC_HUMANDisease (IGKCD)  ---LW148R
3UniProtVAR_003897V84LIGKC_HUMANPolymorphism  ---LV191L
4UniProtVAR_067537R334CNRP2_HUMANPolymorphism114144673AR334C
5UniProtVAR_067538R428WNRP2_HUMANPolymorphism139711818AR428W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (5, 9)

Asymmetric Unit (5, 9)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CUBPS01180 CUB domain profile.NRP2_HUMAN28-142
149-267
  2A:28-142
A:149-267
2IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGKC_HUMAN85-91  1L:192-198
3FA58C_3PS50022 Coagulation factors 5/8 type C domain (FA58C) profile.NRP2_HUMAN277-427
434-592
  2A:277-427
A:434-592
4FA58C_1PS01285 Coagulation factors 5/8 type C domain (FA58C) signature 1.NRP2_HUMAN317-346
473-505
  2A:317-346
A:473-505
5FA58C_2PS01286 Coagulation factors 5/8 type C domain (FA58C) signature 2.NRP2_HUMAN411-427
575-592
  2A:411-427
A:575-592
Biological Unit 1 (5, 18)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CUBPS01180 CUB domain profile.NRP2_HUMAN28-142
149-267
  4A:28-142
A:149-267
2IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGKC_HUMAN85-91  2L:192-198
3FA58C_3PS50022 Coagulation factors 5/8 type C domain (FA58C) profile.NRP2_HUMAN277-427
434-592
  4A:277-427
A:434-592
4FA58C_1PS01285 Coagulation factors 5/8 type C domain (FA58C) signature 1.NRP2_HUMAN317-346
473-505
  4A:317-346
A:473-505
5FA58C_2PS01286 Coagulation factors 5/8 type C domain (FA58C) signature 2.NRP2_HUMAN411-427
575-592
  4A:411-427
A:575-592
Biological Unit 2 (5, 9)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CUBPS01180 CUB domain profile.NRP2_HUMAN28-142
149-267
  2A:28-142
A:149-267
2IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGKC_HUMAN85-91  1L:192-198
3FA58C_3PS50022 Coagulation factors 5/8 type C domain (FA58C) profile.NRP2_HUMAN277-427
434-592
  2A:277-427
A:434-592
4FA58C_1PS01285 Coagulation factors 5/8 type C domain (FA58C) signature 1.NRP2_HUMAN317-346
473-505
  2A:317-346
A:473-505
5FA58C_2PS01286 Coagulation factors 5/8 type C domain (FA58C) signature 2.NRP2_HUMAN411-427
575-592
  2A:411-427
A:575-592

(-) Exons   (9, 9)

Asymmetric Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003604092aENSE00001350724chr2:206547224-206548087864NRP2_HUMAN1-25250--
1.4aENST000003604094aENSE00000796618chr2:206562268-206562445178NRP2_HUMAN25-84601A:27-8458
1.6bENST000003604096bENSE00000796621chr2:206580917-206581098182NRP2_HUMAN84-145621A:84-145 (gaps)62
1.7bENST000003604097bENSE00000796622chr2:206587202-206587432231NRP2_HUMAN145-222781A:145-222 (gaps)78
1.8bENST000003604098bENSE00000796624chr2:206588509-206588664156NRP2_HUMAN222-274531A:222-27453
1.9ENST000003604099ENSE00000796626chr2:206590637-206590806170NRP2_HUMAN274-330571A:274-33057
1.10ENST0000036040910ENSE00000796629chr2:206592615-206592770156NRP2_HUMAN331-382521A:331-38252
1.12ENST0000036040912ENSE00000796630chr2:206605243-206605387145NRP2_HUMAN383-431491A:383-43149
1.13aENST0000036040913aENSE00001238400chr2:206607927-206608276350NRP2_HUMAN431-5471171A:431-547 (gaps)117
1.14ENST0000036040914ENSE00000796635chr2:206610470-206610614145NRP2_HUMAN548-596491A:548-59447
1.15bENST0000036040915bENSE00000796636chr2:206614449-206614565117NRP2_HUMAN596-635400--
1.16bENST0000036040916bENSE00000796638chr2:206617559-206617699141NRP2_HUMAN635-682480--
1.17cENST0000036040917cENSE00000796640chr2:206628398-206628660263NRP2_HUMAN682-769880--
1.19ENST0000036040919ENSE00000796643chr2:206630198-20663029497NRP2_HUMAN770-802330--
1.20bENST0000036040920bENSE00001238223chr2:206631507-20663154236NRP2_HUMAN802-814130--
1.23ENST0000036040923ENSE00000796649chr2:206656959-20665700951NRP2_HUMAN814-831180--
1.24dENST0000036040924dENSE00001350546chr2:206659478-2066628573380NRP2_HUMAN831-9311010--

(-) 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:541
 aligned with NRP2_HUMAN | O60462 from UniProtKB/Swiss-Prot  Length:931

    Alignment length:568
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586        
          NRP2_HUMAN     27 PCGGRLNSKDAGYITSPGYPQDYPSHQNCEWIVYAPEPNQKIVLNFNPHFEIEKHDCKYDFIEIRDGDSESADLLGKHCGNIAPPTIISSGSMLYIRFTSDYARQGAGFSLRYEIFKTGSEDCSKNFTSPNGTIESPGFPEKYPHNLDCTFTILAKPKMEIILQFLIFDLEHDPLQVGEGDCKYDWLDIWDGIPHVGPLIGKYCGTKTPSELRSSTGILSLTFHTDMAVAKDGFSARYYLVHQEPLENFQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNLDSNKEYLQVDLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHKVFQANNDATEVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRVTDAPCSNMLGMLSGLIADSQISASSTQEYLWSPSAARLVSSRSGWFPRIPQAQPGEEWLQVDLGTPKTVKGVIIQGARGGDSITAVEARAFVRKFKVSYSLNGKDWEYIQDPRTQQPKLFEGNMHYDTPDIRRFDPIPAQYVRVYPERWSPAGIGMRLEVLGCDW  594
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qqkA01 A:27-146  [code=2.60.120.290, no name defined]                                                                  2qqkA02 A:147-274  [code=2.60.120.290, no name def             ined]                                                            2qqkA03 A:275-431 Galactose-binding domain-like                                                                                                              2qqkA04 A:432-594 Galactos  e-binding domain-like                                                                                                                   CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------   ------------------CUB-2qqkA01 A:149-264                                                                                               ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------F5_F8_typ  e_C-2qqkA03 A:449-589                                                                                                             ----- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------   ------------------CUB-2qqkA02 A:149-264                                                                                               ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------F5_F8_typ  e_C-2qqkA04 A:449-589                                                                                                             ----- Pfam domains (2)
         Sec.struct. author ...eeee....eeee.............eeeeee......eeeeee..............eeeeee......eeeeee........ee....eeeeeee..---.....eeeeeee.........ee...eeeee............eeeeeee....eeeeeeeeeee.-------------..eeeee........eeeee........eee...eeeeeee........eeeeeeeeee..........ee........hhh.eee.........hhhhh...................eeeeeeeeeeeeeeeee.ee......eeeeeeeeeeee......ee.ee..ee..ee........eeeeeeeeeeeeeeeeeeeeee.....eeeeeeehhhhh...ee........hhh.eee.....--.hhhhhh.....................eeeeeeeeeeeeeeeee...---------....eeeeeeeee......ee...........ee........eeeeeeeeeeeeeeeeeeee.......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------K------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C---------------------------------------------------------------------------------------------W---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -CUB  PDB: A:28-142 UniProt: 28-142                                                                                 ------CUB  PDB: A:149-267 UniProt: 149-267                                                                                   ---------FA58C_3  PDB: A:277-427 UniProt: 277-427                                                                                                               ------FA58C_3  PDB: A:434-592 UniProt: 434-592                                                                                                                       -- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FA58C_1  PDB: A:317-346       ----------------------------------------------------------------FA58C_2          ---------------------------------------------FA58C_1  PDB: A:473-505          ---------------------------------------------------------------------FA58C_2           -- PROSITE (2)
           Transcript 1 (1) Exon 1.4a  PDB: A:27-84 UniProt: 25-84 [INCOMPLETE]       ------------------------------------------------------------Exon 1.7b  PDB: A:145-222 (gaps) UniProt: 145-222                             ---------------------------------------------------Exon 1.9  PDB: A:274-330 UniProt: 274-330                Exon 1.10  PDB: A:331-382 UniProt: 331-382          Exon 1.12  PDB: A:383-431 UniProt: 383-431       --------------------------------------------------------------------------------------------------------------------Exon 1.14  PDB: A:548-594 UniProt: 548-596      Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------Exon 1.6b  PDB: A:84-145 (gaps) UniProt: 84-145               ----------------------------------------------------------------------------Exon 1.8b  PDB: A:222-274 UniProt: 222-274           ------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.13a  PDB: A:431-547 (gaps) UniProt: 431-547                                                                   ----------------------------------------------- Transcript 1 (2)
                2qqk A   27 PCGGRLNSKDAGYITSPGYPQDYPSHQNCEWIVYAPEPNQKIVLNFNPHFEIEKHDCKYDFIEIRDGDSESADLLGKHCGNIAPPTIISSGSMLYIKFTSD---QGAGFSLRYEIFKTGSEDCSKNFTSPNGTIESPGFPEKYPHNLDCTFTILAKPKMEIILQFLIFDL-------------YDWLDIWDGIPHVGPLIGKYCGTKTPSELRSSTGILSLTFHTDMAVAKDGFSARYYLVHQEPLENFQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNLDSNKEYLQVDLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHKVFQANNDATEVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRVTDAPCSNMLGMLSGLIADSQISASSTQE--WSPSAARLVSSRSGWFPRIPQAQPGEEWLQVDLGTPKTVKGVIIQGAR---------ARAFVRKFKVSYSLNGKDWEYIQDPRTQQPKLFEGNMHYDTPDIRRFDPIPAQYVRVYPERWSPAGIGMRLEVLGCDW  594
                                    36        46        56        66        76        86        96       106       116       126|   |  136       146       156       166       176       186       196         -   |   216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456|  |   466       476       486       496       506|        -|      526       536       546       556       566       576       586        
                                                                                                                              127 131                                                              196           210                                                                                                                                                                                                                                                    457  |                                            507       517                                                                             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                           460                                                                                                                                      

Chain H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qqkH01 H:1-113 Immunoglobulins                                                                                             2qqkH02 H:114-220 Immunoglobulins                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeee.....eeeeeeee....eeee.......eeeeee....eeeeee...hhhhheeeeeeee....hhhhh..eeee...eeeee........eeeee....eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeehhhhh.....eeeeehhhhh...eee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2qqk H    1 EVQLVESGGGLVQPGGSLRLSCAASGFTISGYGIHWVRQAPGKGLEWVAYIYPDSGYTDYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCAREDFRNRRRLWYVMDYWGQGTLVTVSSASTKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPTH  220
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|      109       119      |136       146       156       166       176       186       196       206      || 
                                                                              52A                            82A||               100A||||||                       126|                                                                            213| 
                                                                                                              82B|                100B|||||                        134                                                                             219 
                                                                                                               82C                 100C||||                                                                                                            
                                                                                                                                    100D|||                                                                                                            
                                                                                                                                     100E||                                                                                                            
                                                                                                                                      100F|                                                                                                            
                                                                                                                                       100G                                                                                                            

Chain L from PDB  Type:PROTEIN  Length:211
 aligned with IGKC_HUMAN | P01834 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:211
                                                                                                                                       1                                                                                                       
                                     -         -         -         -         -         -         -         -         -         -       | 3        13        23        33        43        53        63        73        83        93       103 
          IGKC_HUMAN      - -----------------------------------------------------------------------------------------------------------RTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  104
               SCOP domains d2qqkl1 L:1-107 automated matches                                                                          d2qqkl2 L:108-211 automated matches                                                                      SCOP domains
               CATH domains 2qqkL01 L:1-108 Immunoglobulins                                                                             2qqkL02 L:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh...eeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeehhhhhhhh..eeeeee.......eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------R------------------------------------------L-------------------- SAPs(SNPs)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2qqk L    1 DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQAWAYLPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 

   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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (3, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: CUB (11)
(-)
Family: CUB (11)
1aCUB-2qqkA01A:149-264
1bCUB-2qqkA02A:149-264
(-)
Clan: GBD (153)

(-) Gene Ontology  (52, 73)

Asymmetric Unit(hide GO term definitions)
Chain A   (NRP2_HUMAN | O60462)
molecular function
    GO:0019955    cytokine binding    Interacting selectively and non-covalently with a cytokine, any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity.
    GO:0019838    growth factor binding    Interacting selectively and non-covalently with any growth factor, proteins or polypeptides that stimulate a cell or organism to grow or proliferate.
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0017154    semaphorin receptor activity    Combining with a semaphorin, and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
    GO:0005021    vascular endothelial growth factor-activated receptor activity    Combining with a vascular endothelial growth factor (VEGF) and transmitting the signal across the plasma membrane to initiate a change in cell activity.
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0048846    axon extension involved in axon guidance    The long distance growth of a single cell process, that is involved in the migration of an axon growth cone, where the migration is directed to a specific target site by a combination of attractive and repulsive cues.
    GO:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0021675    nerve development    The process whose specific outcome is the progression of a nerve over time, from its formation to the mature structure.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0010595    positive regulation of endothelial cell migration    Any process that increases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
    GO:0001938    positive regulation of endothelial cell proliferation    Any process that activates or increases the rate or extent of endothelial cell proliferation.
    GO:1902285    semaphorin-plexin signaling pathway involved in neuron projection guidance    Any semaphorin-plexin signaling pathway that is involved in neuron projection guidance.
    GO:0061549    sympathetic ganglion development    The process whose specific outcome is the progression of a sympathetic ganglion over time, from its formation to the mature structure.
    GO:0097490    sympathetic neuron projection extension    Long distance growth of a single sympathetic neuron projection involved in cellular development. A neuron projection is a prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0097491    sympathetic neuron projection guidance    The process in which the migration of a sympathetic neuron projection is directed to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0048010    vascular endothelial growth factor receptor signaling pathway    Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0038084    vascular endothelial growth factor signaling pathway    A series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a receptor on the surface of the target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0002116    semaphorin receptor complex    A stable binary complex of a neurophilin and a plexin, together forming a functional semaphorin receptor.

Chain L   (IGKC_HUMAN | P01834)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
    GO:0034987    immunoglobulin receptor binding    Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0050853    B cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
    GO:0038095    Fc-epsilon receptor signaling pathway    A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
    GO:0038096    Fc-gamma receptor signaling pathway involved in phagocytosis    An Fc-gamma receptor signaling pathway that contributes to the endocytic engulfment of external particulate material by phagocytes.
    GO:0006956    complement activation    Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.
    GO:0006958    complement activation, classical pathway    Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0006911    phagocytosis, engulfment    The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.
    GO:0006910    phagocytosis, recognition    The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
    GO:0050871    positive regulation of B cell activation    Any process that activates or increases the frequency, rate or extent of B cell activation.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0001895    retina homeostasis    A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function.
cellular component
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0042571    immunoglobulin complex, circulating    An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IGHG1_HUMAN | P018571aj7 1aqk 1axs 1bey 1d5b 1d5i 1d6v 1dfb 1dn2 1e4k 1fc1 1fc2 1fcc 1gaf 1h3t 1h3u 1h3v 1h3w 1h3x 1h3y 1hkl 1hzh 1i7z 1l6x 1n7m 1op3 1oqo 1oqx 1pg7 1t83 1t89 1vge 2dts 2gj7 2i5y 2iwg 2j6e 2jb5 2jb6 2o5x 2o5y 2o5z 2osl 2qad 2ql1 2qql 2qqn 2qr0 2r56 2rcj 2rcs 2vxq 2wah 3agv 3ave 3ay4 3b2u 3b2v 3bdy 3be1 3bky 3bn9 3bqu 3c08 3c09 3c2s 3cfj 3cfk 3csy 3d0l 3d0v 3d6g 3d85 3dj9 3dnk 3do3 3dro 3drq 3dvg 3dvn 3eyf 3eyo 3eyq 3fjt 3mcl 3o11 3ry6 3s7g 3sgj 3sgk 3tv3 3twc 3tyg 3u0w 3u7w 3u7y 3v7m 3v8c 3v95 3wjj 3wjl 3wkn 3wn5 4acp 4b7i 4bm7 4bsv 4bsw 4byh 4cdh 4d9q 4d9r 4dag 4dz8 4eow 4hix 4j12 4ku1 4lld 4llm 4llq 4n0u 4nqs 4nqt 4nqu 4nwt 4nwu 4o4y 4o51 4q6y 4q74 4q7d 4w4n 4w4o 4wi2 4wi3 4wi4 4wi5 4wi6 4wi7 4wi8 4wi9 4x4m 4x98 4x99 4xmp 4xny 4xnz 4xxd 4zne 5bw7 5c7k 5d4q 5d6d 5di8 5dj0 5dj2 5dj6 5dj8 5dja 5djc 5djd 5djx 5djy 5djz 5dk0 5dk2 5dvk 5dvl 5dvm 5dvn 5dvo 5gsq 5hsf 5hy9 5hye 5hyf 5hyi 5iq7 5iq9 5iw3 5iw6 5jih 5jii 5jik 5k33 5k8d 5kwg 5m3v 5v43 5v4e
        IGKC_HUMAN | P018341a4j 1a4k 1cly 1d5b 1d5i 1d6v 1dfb 1gaf 1hez 1hkl 1hzh 1i7z 1mim 1n0x 1om3 1op3 1op5 1ucb 2ny7 2o5x 2o5y 2o5z 2qql 2qqn 2qsc 2r56 2rfx 2vxq 3b2u 3b2v 3bdy 3be1 3bky 3bn9 3bqu 3c08 3c09 3cfj 3cfk 3csy 3d0l 3d85 3dvg 3dvn 3eyf 3eyo 3eyq 3iu3 3o11 3qct 3qcu 3qcv 3ru8 3u0w 3u7w 3u7y 3vh8 3wuw 3x11 3x12 4d3c 4d9r 4hix 4nm4 4nm8 4xmp 4xny 4xnz 4xxd 4ydv 5b38 5b39 5c7k 5esv 5esz 5ewi 5veb 5viy
        NRP2_HUMAN | O604622qqj 2qql 2qqo 4qdq 4qdr 4qds 5dn2 5dq0

(-) Related Entries Specified in the PDB File

2qqi 2qqj 2qql 2qqm 2qqn 2qqo