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(-) Description

Title :  NEUROPSIN, A SERINE PROTEASE EXPRESSED IN THE LIMBIC SYSTEM OF MOUSE BRAIN
 
Authors :  T. Kishi, M. Kato, T. Shimizu, K. Kato, K. Matsumoto, S. Yoshida, S. Shio T. Hakoshima
Date :  07 Jan 98  (Deposition) - 23 Mar 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Serine Proteinase, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Kishi, M. Kato, T. Shimizu, K. Kato, K. Matsumoto, S. Yoshida, S. Shiosaka, T. Hakoshima
Crystal Structure Of Neuropsin, A Hippocampal Protease Involved In Kindling Epileptogenesis.
J. Biol. Chem. V. 274 4220 1999
PubMed-ID: 9933620  |  Reference-DOI: 10.1074/JBC.274.7.4220
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEUROPSIN
    Cell LineHIGH5
    ChainsA, B
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineHIGH5
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPVL1392
    Expression System Taxid7108
    Expression System VectorBACULOVIRUS
    OrganHIPPOCAMPUS
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 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
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:95 , ASN A:95CBINDING SITE FOR RESIDUE NAG A 501
2AC2SOFTWAREASN B:95 , SER B:95B , ASN B:95CBINDING SITE FOR RESIDUE NAG B 501
3ACAUNKNOWNHIS A:57 , ASP A:102 , SER A:195CATALYTIC TRIAD (ACTIVE SITE).
4ACBUNKNOWNHIS B:57 , ASP B:102 , SER B:195CATALYTIC TRIAD (ACTIVE SITE).

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:22 -A:157
2A:42 -A:58
3A:128 -A:232
4A:136 -A:201
5A:168 -A:182
6A:191 -A:220
7B:22 -B:157
8B:42 -B:58
9B:128 -B:232
10B:136 -B:201
11B:168 -B:182
12B:191 -B:220

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:146 -Pro A:147
2Asp A:218 -Pro A:219
3Ser B:146 -Pro B:147
4Asp B:218 -Pro B:219

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NPM)

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.KLK8_MOUSE33-257
 
  2A:16-243
B:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.KLK8_MOUSE69-74
 
  2A:53-58
B:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.KLK8_MOUSE206-217
 
  2A:189-200
B:189-200
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.KLK8_MOUSE33-257
 
  1A:16-243
-
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.KLK8_MOUSE69-74
 
  1A:53-58
-
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.KLK8_MOUSE206-217
 
  1A:189-200
-
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.KLK8_MOUSE33-257
 
  1-
B:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.KLK8_MOUSE69-74
 
  1-
B:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.KLK8_MOUSE206-217
 
  1-
B:189-200

(-) Exons   (0, 0)

(no "Exon" information available for 1NPM)

(-) 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:223
 aligned with KLK8_MOUSE | Q61955 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:225
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252     
          KLK8_MOUSE     33 ILEGRECIPHSQPWQAALFQGERLICGGVLVGDRWVLTAAHCKKQKYSVRLGDHSLQSRDQPEQEIQVAQSIQHPCYNNSNPEDHSHDIMLIRLQNSANLGDKVKPVQLANLCPKVGQKCIISGWGTVTSPQENFPNTLNCAEVKIYSQNKCERAYPGKITEGMVCAGSSNGADTCQGDSGGPLVCDGMLQGITSWGSDPCGKPEKPGVYTKICRYTTWIKKTMD  257
               SCOP domains d1npma_ A: Neuropsin                                                                                                                                                                                                              SCOP domains
               CATH domains 1npmA01     1npmA02 A:28-120,A:233-242 Trypsin-like serine   proteases                                    1npmA01 A:16-27,A:121-232 Trypsin-like serine proteases                                                     1npmA02   - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeeee.eeeee.hhh.....eeee.......--...eeeeeeeeee................eeeeee............ee.........eeeeee...............eeeeeee..hhhhhhh........eeeee..............eeee..eeeeeeee...........eeeeehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 33-257                                                                                                                                                                                        PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI-----------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ---------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1npm A   16 ILEGRECIPHSQPWQAALFQGERLICGGVLVGDRWVLTAAHCKKQKYSVRLGDHSLQS--QPEQEIQVAQSIQHPCYNNSNPEDHSHDIMLIRLQNSANLGDKVKPVQLANLCPKVGQKCIISGWGTVTSPQENFPNTLNCAEVKIYSQNKCERAYPGKITEGMVCAGSSNGADTCQGDSGGPLVCDGMLQGITSWGSDPCGKPEKPGVYTKICRYTTWIKKTMD  243
                                    25        35||      46        56        66||     | -|       87       95B|||    104       114       124||  || 136       146       156       166       176       186|      195       209       219 |     228       238     
                                               36|                           67|    75 78               95A||||                         125|  ||                                                   186A              203|         220A                       
                                                38                            69                         95B|||                          127  ||                                                                      208                                    
                                                                                                          95C||                             130|                                                                                                             
                                                                                                           95D|                              132                                                                                                             
                                                                                                             97                                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:223
 aligned with KLK8_MOUSE | Q61955 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:225
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252     
          KLK8_MOUSE     33 ILEGRECIPHSQPWQAALFQGERLICGGVLVGDRWVLTAAHCKKQKYSVRLGDHSLQSRDQPEQEIQVAQSIQHPCYNNSNPEDHSHDIMLIRLQNSANLGDKVKPVQLANLCPKVGQKCIISGWGTVTSPQENFPNTLNCAEVKIYSQNKCERAYPGKITEGMVCAGSSNGADTCQGDSGGPLVCDGMLQGITSWGSDPCGKPEKPGVYTKICRYTTWIKKTMD  257
               SCOP domains d1npmb_ B: Neuropsin                                                                                                                                                                                                              SCOP domains
               CATH domains 1npmB01     1npmB02 B:28-120,B:233-242 Trypsin-like serine   proteases                                    1npmB01 B:16-27,B:121-232 Trypsin-like serine proteases                                                     1npmB02   - CATH domains
           Pfam domains (1) Trypsin-1npmB01 B:16-238                                                                                                                                                                                                    ----- Pfam domains (1)
           Pfam domains (2) Trypsin-1npmB02 B:16-238                                                                                                                                                                                                    ----- Pfam domains (2)
         Sec.struct. author ....ee........eeeeee..eeeeeeeeee.eeeee.hhh.....eeee.......--...eeeeeeeeee................eeeeee............ee.........eeeeee...............eeeeeee..hhhhhhh........eeeee..............eeee..eeeeeeee...........eeeeehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:16-243 UniProt: 33-257                                                                                                                                                                                        PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI-----------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ---------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1npm B   16 ILEGRECIPHSQPWQAALFQGERLICGGVLVGDRWVLTAAHCKKQKYSVRLGDHSLQS--QPEQEIQVAQSIQHPCYNNSNPEDHSHDIMLIRLQNSANLGDKVKPVQLANLCPKVGQKCIISGWGTVTSPQENFPNTLNCAEVKIYSQNKCERAYPGKITEGMVCAGSSNGADTCQGDSGGPLVCDGMLQGITSWGSDPCGKPEKPGVYTKICRYTTWIKKTMD  243
                                    25        35||      46        56        66||     | -|       87       95B|||    104       114       124||  || 136       146       156       166       176       186|      195       209       219 |     228       238     
                                               36|                           67|    75 78               95A||||                         125|  ||                                                   186A              203|         220A                       
                                                38                            69                         95B|||                          127  ||                                                                      208                                    
                                                                                                          95C||                             130|                                                                                                             
                                                                                                           95D|                              132                                                                                                             
                                                                                                             97                                                                                                                                              

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
1a1npmA01A:16-27,A:121-232
1b1npmB01B:16-27,B:121-232
1c1npmA02A:28-120,A:233-242
1d1npmB02B:28-120,B:233-242

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KLK8_MOUSE | Q61955)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of 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:0008219    cell death    Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538).
    GO:0043616    keratinocyte proliferation    The multiplication or reproduction of keratinocytes, resulting in the expansion of a cell population. Keratinocytes are epidermal cells which synthesize keratin and undergo a characteristic change as they move upward from the basal layers of the epidermis to the cornified (horny) layer of the skin.
    GO:0007613    memory    The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).
    GO:0048681    negative regulation of axon regeneration    Any process that stops, prevents, or reduces the frequency, rate or extent of axon regeneration.
    GO:0031642    negative regulation of myelination    Any process that stops, prevents, or reduces the frequency, rate or extent of the formation of a myelin sheath around nerve axons.
    GO:0048812    neuron projection morphogenesis    The process in which the anatomical structures of a neuron projection are generated and organized. A neuron projection is any process extending from a neural cell, such as axons or dendrites.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0050807    regulation of synapse organization    Any process that modulates the physical form of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell).
    GO:0009611    response to wounding    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
    GO:0050808    synapse organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

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