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(-) Description

Title :  CRYSTAL STRUCTURE OF STEFIN A IN COMPLEX WITH CATHEPSIN H: N-TERMINAL RESIDUES OF INHIBITORS CAN ADAPT TO THE ACTIVE SITES OF ENDO-AND EXOPEPTIDASES
 
Authors :  S. Jenko, I. Dolenc, G. Guncar, A. Dobersek, M. Podobnik, D. Turk
Date :  02 Dec 02  (Deposition) - 18 Feb 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,I,J,K,L,P,R,S,T
Biol. Unit 1:  A,I,P  (1x)
Biol. Unit 2:  B,J,R  (1x)
Biol. Unit 3:  C,K,S  (1x)
Biol. Unit 4:  D,L,T  (1x)
Keywords :  Cysteine Proteinase, Aminopeptidase, Cystatin, Enzyme-Inhibitor Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Jenko, I. Dolenc, G. Guncar, A. Dobersek, M. Podobnik, D. Turk
Crystal Structure Of Stefin A In Complex With Cathepsin H: N-Terminal Residues Of Inhibitors Can Adapt To The Active Sites Of Endo- And Exopeptidases
J. Mol. Biol. V. 326 875 2003
PubMed-ID: 12581647  |  Reference-DOI: 10.1016/S0022-2836(02)01432-8

(-) Compounds

Molecule 1 - CATHEPSIN H
    ChainsA, B, C, D
    EC Number3.4.22.16
    Organism CommonPIG
    Organism ScientificSUS SCROFA
    Organism Taxid9823
    Other DetailsPROTEIN WAS ISOLATED FROM SPLEEN
 
Molecule 2 - CATHEPSIN H MINI CHAIN
    ChainsP, R, S, T
    EC Number3.4.22.16
    Organism CommonPIG
    Organism ScientificSUS SCROFA
    Organism Taxid9823
    Other DetailsPROTEIN WAS ISOLATED FROM SPLEEN
 
Molecule 3 - STEFIN A
    ChainsI, J, K, L
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET3A
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneCSTA OR STF1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCYSTATIN AS, CYSTATIN A

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit ABCDIJKLPRST
Biological Unit 1 (1x)A   I   P   
Biological Unit 2 (1x) B   J   R  
Biological Unit 3 (1x)  C   K   S 
Biological Unit 4 (1x)   D   L   T

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:69 , GLU A:73 , ASN A:112 , NAG A:214 , GLU P:76 , PRO P:77 , GLN P:78BINDING SITE FOR RESIDUE NAG A 213
02AC2SOFTWAREPHE A:58B , GLN A:70 , GLU A:73 , NAG A:213 , BMA A:215BINDING SITE FOR RESIDUE NAG A 214
03AC3SOFTWARETYR A:77 , NAG A:214 , HOH A:252BINDING SITE FOR RESIDUE BMA A 215
04AC4SOFTWARESER B:69 , GLN B:70 , GLU B:73 , ASN B:112 , NAG B:214 , GLU R:76 , PRO R:77 , GLN R:78BINDING SITE FOR RESIDUE NAG B 213
05AC5SOFTWAREPHE B:58B , GLN B:70 , GLU B:73 , TYR B:77 , NAG B:213 , BMA B:215BINDING SITE FOR RESIDUE NAG B 214
06AC6SOFTWAREPHE B:58B , TYR B:77 , NAG B:214 , HOH B:310 , HOH B:324BINDING SITE FOR RESIDUE BMA B 215
07AC7SOFTWAREGLU C:73 , ASN C:112 , NAG C:214 , GLU S:76 , PRO S:77 , GLN S:78BINDING SITE FOR RESIDUE NAG C 213
08AC8SOFTWAREPHE C:58B , GLN C:70 , GLU C:73 , TYR C:77 , NAG C:213 , BMA C:215BINDING SITE FOR RESIDUE NAG C 214
09AC9SOFTWAREPHE C:58B , TYR C:77 , NAG C:214 , HOH C:252 , HOH C:266BINDING SITE FOR RESIDUE BMA C 215
10BC1SOFTWAREGLU D:73 , ASN D:112 , NAG D:214 , GLU T:76 , PRO T:77 , GLN T:78BINDING SITE FOR RESIDUE NAG D 213
11BC2SOFTWAREPHE D:58B , GLN D:70 , GLU D:73 , TYR D:77 , NAG D:213 , BMA D:215BINDING SITE FOR RESIDUE NAG D 214
12BC3SOFTWARETYR D:77 , NAG D:214 , HOH D:293 , HOH D:298BINDING SITE FOR RESIDUE BMA D 215

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:22 -A:63
2A:56 -A:95
3A:154 -A:200
4A:205 -P:80
5B:22 -B:63
6B:56 -B:95
7B:154 -B:200
8B:205 -R:80
9C:22 -C:63
10C:56 -C:95
11C:154 -C:200
12C:205 -S:80
13D:22 -D:63
14D:56 -D:95
15D:154 -D:200
16D:205 -T:80

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NB3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 4)

Asymmetric Unit (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048851T96MCYTA_HUMANPolymorphism34173813I/J/K/LT123M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048851T96MCYTA_HUMANPolymorphism34173813IT123M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048851T96MCYTA_HUMANPolymorphism34173813JT123M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048851T96MCYTA_HUMANPolymorphism34173813KT123M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 4 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048851T96MCYTA_HUMANPolymorphism34173813LT123M

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

(-) PROSITE Motifs  (4, 16)

Asymmetric Unit (4, 16)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYSTATINPS00287 Cysteine proteases inhibitors signature.CYTA_HUMAN45-58
 
 
 
  4I:52-65
J:52-65
K:52-65
L:52-65
2THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.CATH_PIG135-146
 
 
 
  4A:19-30
B:19-30
C:19-30
D:19-30
3THIOL_PROTEASE_HISPS00639 Eukaryotic thiol (cysteine) proteases histidine active site.CATH_PIG279-289
 
 
 
  4A:157-167
B:157-167
C:157-167
D:157-167
4THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.CATH_PIG296-315
 
 
 
  4A:170-189
B:170-189
C:170-189
D:170-189
Biological Unit 1 (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYSTATINPS00287 Cysteine proteases inhibitors signature.CYTA_HUMAN45-58
 
 
 
  1I:52-65
-
-
-
2THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.CATH_PIG135-146
 
 
 
  1A:19-30
-
-
-
3THIOL_PROTEASE_HISPS00639 Eukaryotic thiol (cysteine) proteases histidine active site.CATH_PIG279-289
 
 
 
  1A:157-167
-
-
-
4THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.CATH_PIG296-315
 
 
 
  1A:170-189
-
-
-
Biological Unit 2 (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYSTATINPS00287 Cysteine proteases inhibitors signature.CYTA_HUMAN45-58
 
 
 
  1-
J:52-65
-
-
2THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.CATH_PIG135-146
 
 
 
  1-
B:19-30
-
-
3THIOL_PROTEASE_HISPS00639 Eukaryotic thiol (cysteine) proteases histidine active site.CATH_PIG279-289
 
 
 
  1-
B:157-167
-
-
4THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.CATH_PIG296-315
 
 
 
  1-
B:170-189
-
-
Biological Unit 3 (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYSTATINPS00287 Cysteine proteases inhibitors signature.CYTA_HUMAN45-58
 
 
 
  1-
-
K:52-65
-
2THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.CATH_PIG135-146
 
 
 
  1-
-
C:19-30
-
3THIOL_PROTEASE_HISPS00639 Eukaryotic thiol (cysteine) proteases histidine active site.CATH_PIG279-289
 
 
 
  1-
-
C:157-167
-
4THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.CATH_PIG296-315
 
 
 
  1-
-
C:170-189
-
Biological Unit 4 (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYSTATINPS00287 Cysteine proteases inhibitors signature.CYTA_HUMAN45-58
 
 
 
  1-
-
-
L:52-65
2THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.CATH_PIG135-146
 
 
 
  1-
-
-
D:19-30
3THIOL_PROTEASE_HISPS00639 Eukaryotic thiol (cysteine) proteases histidine active site.CATH_PIG279-289
 
 
 
  1-
-
-
D:157-167
4THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.CATH_PIG296-315
 
 
 
  1-
-
-
D:170-189

(-) Exons   (3, 12)

Asymmetric Unit (3, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002644741aENSE00001154693chr3:122044091-122044205115CYTA_HUMAN1-22224I:6-27
J:6-27
K:6-27
L:6-27
22
22
22
22
1.2aENST000002644742aENSE00001078746chr3:122056394-122056495102CYTA_HUMAN23-56344I:28-63 (gaps)
J:28-63 (gaps)
K:28-63 (gaps)
L:28-63 (gaps)
36
36
36
36
1.3ENST000002644743ENSE00001154683chr3:122060286-122060819534CYTA_HUMAN57-98424I:64-125 (gaps)
J:64-125 (gaps)
K:64-125 (gaps)
L:64-125 (gaps)
65
65
65
65

(-) 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:220
 aligned with CATH_PIG | O46427 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:220
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335
            CATH_PIG    116 YPPSMDWRKKGNFVSPVKNQGSCGSCWTFSTTGALESAVAIATGKMLSLAEQQLVDCAQNFNNHGCQGGLPSQAFEYIRYNKGIMGEDTYPYKGQDDHCKFQPDKAIAFVKDVANITMNDEEAMVEAVALYNPVSFAFEVTNDFLMYRKGIYSSTSCHKTPDKVNHAVLAVGYGEENGIPYWIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPIPLV  335
               SCOP domains d1nb3.1 P:,A: Cathepsin H                                                                                                                                                                                                    SCOP domains
               CATH domains 1nb3A00 A:1-212A Cysteine proteinases                                                                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhhhh.............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhh....hhhhh...........hhhhh...eeeeee....hhhhhhhhhhhh..eeeee..hhhhhhh...ee............................................eeeee...hhhhh....eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------THIOL_PROTEASE_ASN  -------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1nb3 A    1 YPPSMDWRKKGNFVSPVKNQGSCGSCWTFSTTGALESAVAIATGKMLSLAEQQLVDCAQNFNNHGCQGGLPSQAFEYIRYNKGIMGEDTYPYKGQDDHCKFQPDKAIAFVKDVANITMNDEEAMVEAVALYNPVSFAFEVTNDFLMYRKGIYSSTSCHKTPDKVNHAVLAVGYGEENGIPYWIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPIPLV 212A
                                    10|       19        29        39        49       58A|       67        77 |      86        96  |||  107       117      126A       136|      147      155B||     163     ||169       179       189  |||  203      212A
                                    10A                                              58A|                  78A                   99||                     126A       136|              155A|||          168A|||                     192||           212A
                                                                                      58B                                        102|                                 138               155B||           168B||                      195|               
                                                                                                                                 102A                                                    155C|            168C|                       198               
                                                                                                                                                                                          155D             168D                                         

Chain B from PDB  Type:PROTEIN  Length:220
 aligned with CATH_PIG | O46427 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:220
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335
            CATH_PIG    116 YPPSMDWRKKGNFVSPVKNQGSCGSCWTFSTTGALESAVAIATGKMLSLAEQQLVDCAQNFNNHGCQGGLPSQAFEYIRYNKGIMGEDTYPYKGQDDHCKFQPDKAIAFVKDVANITMNDEEAMVEAVALYNPVSFAFEVTNDFLMYRKGIYSSTSCHKTPDKVNHAVLAVGYGEENGIPYWIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPIPLV  335
               SCOP domains d1nb3.2 R:,B: Cathepsin H                                                                                                                                                                                                    SCOP domains
               CATH domains 1nb3B00 B:1-212A Cysteine proteinases                                                                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..................hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhh...hhhhh...........hhhhh.....eeeee...hhhhhhhhhhhh..eeeee..hhhhhhh...ee............................................eeeee...hhhhh...eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------THIOL_PROTEASE_ASN  -------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1nb3 B    1 YPPSMDWRKKGNFVSPVKNQGSCGSCWTFSTTGALESAVAIATGKMLSLAEQQLVDCAQNFNNHGCQGGLPSQAFEYIRYNKGIMGEDTYPYKGQDDHCKFQPDKAIAFVKDVANITMNDEEAMVEAVALYNPVSFAFEVTNDFLMYRKGIYSSTSCHKTPDKVNHAVLAVGYGEENGIPYWIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPIPLV 212A
                                    10|       19        29        39        49       58A|       67        77 |      86        96  |||  107       117      126A       136|      147      155B||     163     ||169       179       189  |||  203      212A
                                    10A                                              58A|                  78A                   99||                     126A       136|              155A|||          168A|||                     192||           212A
                                                                                      58B                                        102|                                 138               155B||           168B||                      195|               
                                                                                                                                 102A                                                    155C|            168C|                       198               
                                                                                                                                                                                          155D             168D                                         

Chain C from PDB  Type:PROTEIN  Length:220
 aligned with CATH_PIG | O46427 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:220
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335
            CATH_PIG    116 YPPSMDWRKKGNFVSPVKNQGSCGSCWTFSTTGALESAVAIATGKMLSLAEQQLVDCAQNFNNHGCQGGLPSQAFEYIRYNKGIMGEDTYPYKGQDDHCKFQPDKAIAFVKDVANITMNDEEAMVEAVALYNPVSFAFEVTNDFLMYRKGIYSSTSCHKTPDKVNHAVLAVGYGEENGIPYWIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPIPLV  335
               SCOP domains d1nb3.3 S:,C: Cathepsin H                                                                                                                                                                                                    SCOP domains
               CATH domains 1nb3C00 C:1-212A Cysteine proteinases                                                                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..................hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhh..ee................hhh.eee.eeeeeee...hhhhhhhhhhhh..eeee...hhhhhh....ee..............eeeeeeeee....eeeeee...........eeeee...hhhhh...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------THIOL_PROTEASE_ASN  -------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1nb3 C    1 YPPSMDWRKKGNFVSPVKNQGSCGSCWTFSTTGALESAVAIATGKMLSLAEQQLVDCAQNFNNHGCQGGLPSQAFEYIRYNKGIMGEDTYPYKGQDDHCKFQPDKAIAFVKDVANITMNDEEAMVEAVALYNPVSFAFEVTNDFLMYRKGIYSSTSCHKTPDKVNHAVLAVGYGEENGIPYWIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPIPLV 212A
                                    10|       19        29        39        49       58A|       67        77 |      86        96  |||  107       117      126A       136|      147      155B||     163     ||169       179       189  |||  203      212A
                                    10A                                              58A|                  78A                   99||                     126A       136|              155A|||          168A|||                     192||           212A
                                                                                      58B                                        102|                                 138               155B||           168B||                      195|               
                                                                                                                                 102A                                                    155C|            168C|                       198               
                                                                                                                                                                                          155D             168D                                         

Chain D from PDB  Type:PROTEIN  Length:220
 aligned with CATH_PIG | O46427 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:220
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335
            CATH_PIG    116 YPPSMDWRKKGNFVSPVKNQGSCGSCWTFSTTGALESAVAIATGKMLSLAEQQLVDCAQNFNNHGCQGGLPSQAFEYIRYNKGIMGEDTYPYKGQDDHCKFQPDKAIAFVKDVANITMNDEEAMVEAVALYNPVSFAFEVTNDFLMYRKGIYSSTSCHKTPDKVNHAVLAVGYGEENGIPYWIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPIPLV  335
               SCOP domains d1nb3.4 T:,D: Cathepsin H                                                                                                                                                                                                    SCOP domains
               CATH domains 1nb3D00 D:1-212A Cysteine proteinases                                                                                                                                                                                        CATH domains
           Pfam domains (1) Peptidase_C1-1nb3D01 D:1-210                                                                                                                                                                                             --- Pfam domains (1)
           Pfam domains (2) Peptidase_C1-1nb3D02 D:1-210                                                                                                                                                                                             --- Pfam domains (2)
           Pfam domains (3) Peptidase_C1-1nb3D03 D:1-210                                                                                                                                                                                             --- Pfam domains (3)
           Pfam domains (4) Peptidase_C1-1nb3D04 D:1-210                                                                                                                                                                                             --- Pfam domains (4)
         Sec.struct. author ....eehhhhh.............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhh...................hhhhh.....eeee....hhhhhhhhhhhh..eeeee..hhhhhh.............hhhhh................................eeeee...hhhhh....eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------THIOL_PROTEASE_ASN  -------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1nb3 D    1 YPPSMDWRKKGNFVSPVKNQGSCGSCWTFSTTGALESAVAIATGKMLSLAEQQLVDCAQNFNNHGCQGGLPSQAFEYIRYNKGIMGEDTYPYKGQDDHCKFQPDKAIAFVKDVANITMNDEEAMVEAVALYNPVSFAFEVTNDFLMYRKGIYSSTSCHKTPDKVNHAVLAVGYGEENGIPYWIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPIPLV 212A
                                    10|       19        29        39        49       58A|       67        77 |      86        96  |||  107       117      126A       136|      147      155B||     163     ||169       179       189  |||  203      212A
                                    10A                                              58A|                  78A                   99||                     126A       136|              155A|||          168A|||                     192||           212A
                                                                                      58B                                        102|                                 138               155B||           168B||                      195|               
                                                                                                                                 102A                                                    155C|            168C|                       198               
                                                                                                                                                                                          155D             168D                                         

Chain I from PDB  Type:PROTEIN  Length:98
 aligned with CYTA_HUMAN | P01040 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:98
                                    10        20        30        40        50        60        70        80        90        
          CYTA_HUMAN      1 MIPGGLSEAKPATPEIQEIVDKVKPQLEEKTNETYGKLEAVQYKTQVVAGTNYYIKVRAGDNKYMHLKVFKSLPGQNEDLVLTGYQVDKNKDDELTGF   98
               SCOP domains d1nb3i_ I: Cystatin A (stefin A)                                                                   SCOP domains
               CATH domains 1nb3I00 I:6-125  [code=3.10.450.10, no name defined]                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee.hhhhhhhhhhhhhhhhhhhh......eeeeeeeee...eeeeeeee.....eeeeeeee.........eeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------M-- SAPs(SNPs)
                    PROSITE --------------------------------------------CYSTATIN      ---------------------------------------- PROSITE
               Transcript 1 Exon 1.1a  PDB: I:6-27Exon 1.2a  PDB: I:28-63 (gaps)    Exon 1.3  PDB: I:64-125 (gaps)             Transcript 1
                1nb3 I    6 MIPGGLSEAKPATPEIQEIVDKVKPQLEEKTNETYGKLEAVQYKTQVVAGTNYYIKVRAGDNKYMHLKVFKSLPGQNEDLVLTGYQVDKNKDDELTGF  125
                                    15        25        35    ||  47        57        67||     100  |   |108       117        
                                                             40|                       68|       102A   |       115A          
                                                              43                        92           105A                     

Chain J from PDB  Type:PROTEIN  Length:98
 aligned with CYTA_HUMAN | P01040 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:98
                                    10        20        30        40        50        60        70        80        90        
          CYTA_HUMAN      1 MIPGGLSEAKPATPEIQEIVDKVKPQLEEKTNETYGKLEAVQYKTQVVAGTNYYIKVRAGDNKYMHLKVFKSLPGQNEDLVLTGYQVDKNKDDELTGF   98
               SCOP domains d1nb3j_ J: Cystatin A (stefin A)                                                                   SCOP domains
               CATH domains 1nb3J00 J:6-125  [code=3.10.450.10, no name defined]                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee.hhhhhhhhhhhhhhhhhhhh......eeeeeeeee..eeeeeeeeee...eeeeeeeeee.......eeeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------M-- SAPs(SNPs)
                    PROSITE --------------------------------------------CYSTATIN      ---------------------------------------- PROSITE
               Transcript 1 Exon 1.1a  PDB: J:6-27Exon 1.2a  PDB: J:28-63 (gaps)    Exon 1.3  PDB: J:64-125 (gaps)             Transcript 1
                1nb3 J    6 MIPGGLSEAKPATPEIQEIVDKVKPQLEEKTNETYGKLEAVQYKTQVVAGTNYYIKVRAGDNKYMHLKVFKSLPGQNEDLVLTGYQVDKNKDDELTGF  125
                                    15        25        35    ||  47        57        67||     100  |   |108       117        
                                                             40|                       68|       102A   |       115A          
                                                              43                        92           105A                     

Chain K from PDB  Type:PROTEIN  Length:98
 aligned with CYTA_HUMAN | P01040 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:98
                                    10        20        30        40        50        60        70        80        90        
          CYTA_HUMAN      1 MIPGGLSEAKPATPEIQEIVDKVKPQLEEKTNETYGKLEAVQYKTQVVAGTNYYIKVRAGDNKYMHLKVFKSLPGQNEDLVLTGYQVDKNKDDELTGF   98
               SCOP domains d1nb3k_ K: Cystatin A (stefin A)                                                                   SCOP domains
               CATH domains 1nb3K00 K:6-125  [code=3.10.450.10, no name defined]                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee.hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeee...eeeeeeeee...eeeeeeee..........eeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------M-- SAPs(SNPs)
                    PROSITE --------------------------------------------CYSTATIN      ---------------------------------------- PROSITE
               Transcript 1 Exon 1.1a  PDB: K:6-27Exon 1.2a  PDB: K:28-63 (gaps)    Exon 1.3  PDB: K:64-125 (gaps)             Transcript 1
                1nb3 K    6 MIPGGLSEAKPATPEIQEIVDKVKPQLEEKTNETYGKLEAVQYKTQVVAGTNYYIKVRAGDNKYMHLKVFKSLPGQNEDLVLTGYQVDKNKDDELTGF  125
                                    15        25        35    ||  47        57        67||     100  |   |108       117        
                                                             40|                       68|       102A   |       115A          
                                                              43                        92           105A                     

Chain L from PDB  Type:PROTEIN  Length:98
 aligned with CYTA_HUMAN | P01040 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:98
                                    10        20        30        40        50        60        70        80        90        
          CYTA_HUMAN      1 MIPGGLSEAKPATPEIQEIVDKVKPQLEEKTNETYGKLEAVQYKTQVVAGTNYYIKVRAGDNKYMHLKVFKSLPGQNEDLVLTGYQVDKNKDDELTGF   98
               SCOP domains d1nb3l_ L: Cystatin A (stefin A)                                                                   SCOP domains
               CATH domains 1nb3L00 L:6-125  [code=3.10.450.10, no name defined]                                               CATH domains
           Pfam domains (1) ---Cystatin-1nb3L01 L:9-119                                                                 ------ Pfam domains (1)
           Pfam domains (2) ---Cystatin-1nb3L02 L:9-119                                                                 ------ Pfam domains (2)
           Pfam domains (3) ---Cystatin-1nb3L03 L:9-119                                                                 ------ Pfam domains (3)
           Pfam domains (4) ---Cystatin-1nb3L04 L:9-119                                                                 ------ Pfam domains (4)
         Sec.struct. author .........ee.hhhhhhhhhhhhhhhhhhhh......eeeeeeeee...eeeeeeeee...eeeeeeeee........eeeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------M-- SAPs(SNPs)
                    PROSITE --------------------------------------------CYSTATIN      ---------------------------------------- PROSITE
               Transcript 1 Exon 1.1a  PDB: L:6-27Exon 1.2a  PDB: L:28-63 (gaps)    Exon 1.3  PDB: L:64-125 (gaps)             Transcript 1
                1nb3 L    6 MIPGGLSEAKPATPEIQEIVDKVKPQLEEKTNETYGKLEAVQYKTQVVAGTNYYIKVRAGDNKYMHLKVFKSLPGQNEDLVLTGYQVDKNKDDELTGF  125
                                    15        25        35    ||  47        57        67||     100  |   |108       117        
                                                             40|                       68|       102A   |       115A          
                                                              43                        92           105A                     

Chain P from PDB  Type:PROTEIN  Length:8
 aligned with CATH_PIG | O46427 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:8
            CATH_PIG     98 EPQNCSAT  105
               SCOP domains d1nb3.1  SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                1nb3 P   76 EPQNCSAT   83

Chain R from PDB  Type:PROTEIN  Length:8
 aligned with CATH_PIG | O46427 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:8
            CATH_PIG     98 EPQNCSAT  105
               SCOP domains d1nb3.2  SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                1nb3 R   76 EPQNCSAT   83

Chain S from PDB  Type:PROTEIN  Length:8
 aligned with CATH_PIG | O46427 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:8
            CATH_PIG     98 EPQNCSAT  105
               SCOP domains d1nb3.3  SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                1nb3 S   76 EPQNCSAT   83

Chain T from PDB  Type:PROTEIN  Length:8
 aligned with CATH_PIG | O46427 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:8
            CATH_PIG     98 EPQNCSAT  105
               SCOP domains d1nb3.4  SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                1nb3 T   76 EPQNCSAT   83

   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, 8)

Asymmetric Unit

(-) CATH Domains  (2, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: Cystatin (20)

(-) Gene Ontology  (59, 61)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,P,R,S,T   (CATH_PIG | O46427)
molecular function
    GO:0030108    HLA-A specific activating MHC class I receptor activity    Combining with a MHC class I molecule of the HLA-A subclass to mediate signaling that activates a lymphocyte.
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
    GO:0008656    cysteine-type endopeptidase activator activity involved in apoptotic process    Increases the rate of proteolysis catalyzed by a cysteine-type endopeptidase involved in the apoptotic process.
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    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:0016505    peptidase activator activity involved in apoptotic process    Increases the activity of a peptidase that is involved in the apoptotic process.
    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:0070324    thyroid hormone binding    Interacting selectively and non-covalently with thyroxine (T4) or triiodothyronine (T3), tyrosine-based hormones produced by the thyroid gland.
biological process
    GO:0070371    ERK1 and ERK2 cascade    An intracellular protein kinase cascade containing at least ERK1 or ERK2 (MAPKs), a MEK (a MAPKK) and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0001913    T cell mediated cytotoxicity    The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors.
    GO:0006919    activation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
    GO:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    GO:0010815    bradykinin catabolic process    The chemical reactions and pathways resulting in the breakdown of the peptide bradykinin.
    GO:0097067    cellular response to thyroid hormone stimulus    A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a thyroid hormone stimulus.
    GO:0060448    dichotomous subdivision of terminal units involved in lung branching    The process in which a lung bud bifurcates.
    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:0002764    immune response-regulating signaling pathway    The cascade of processes by which a signal interacts with a receptor, causing a change in the level or activity of a second messenger or other downstream target, and ultimately leading to the activation, perpetuation, or inhibition of an immune response.
    GO:0033619    membrane protein proteolysis    The proteolytic cleavage of a transmembrane protein leading to the release of its intracellular or ecto-domains.
    GO:0001656    metanephros development    The process whose specific outcome is the progression of the metanephros over time, from its formation to the mature structure. In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0010813    neuropeptide catabolic process    The chemical reactions and pathways resulting in the breakdown of neuropeptides. Neuropeptides are signaling peptides that travel across a synaptic junction.
    GO:0045766    positive regulation of angiogenesis    Any process that activates or increases angiogenesis.
    GO:2001235    positive regulation of apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of apoptotic signaling pathway.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0010634    positive regulation of epithelial cell migration    Any process that activates or increases the frequency, rate or extent of epithelial cell migration.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0010952    positive regulation of peptidase activity    Any process that increases the frequency, rate or extent of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0031648    protein destabilization    Any process that decreases the stability of a protein, making it more vulnerable to degradative processes or aggregation.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0051603    proteolysis involved in cellular protein catabolic process    The hydrolysis of a peptide bond or bonds within a protein as part of the chemical reactions and pathways resulting in the breakdown of a protein by individual cells.
    GO:0032526    response to retinoic acid    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 retinoic acid stimulus.
    GO:0043129    surfactant homeostasis    Any process involved in the maintenance of a steady-state level of the surface-active lipoprotein mixture which coats the alveoli.
    GO:0031638    zymogen activation    The proteolytic processing of an inactive enzyme to an active form.
cellular component
    GO:0097208    alveolar lamellar body    A specialized secretory organelle found in type II pneumocytes and involved in the synthesis, secretion, and reutilization of pulmonary surfactant.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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: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:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.

Chain I,J,K,L   (CYTA_HUMAN | P01040)
molecular function
    GO:0004869    cysteine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of a cysteine-type endopeptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0004866    endopeptidase inhibitor activity    Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    GO:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
    GO:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    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:0030216    keratinocyte differentiation    The process in which a relatively unspecialized cell acquires specialized features of a keratinocyte.
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0045861    negative regulation of proteolysis    Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
    GO:0018149    peptide cross-linking    The formation of a covalent cross-link between or within protein chains.
    GO:0016337    single organismal cell-cell adhesion    The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism.
cellular component
    GO:0001533    cornified envelope    A type of plasma membrane that has been modified through addition of distinct intracellular and extracellular components, including ceramide, found in cornifying epithelial cells (corneocytes).
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CATH_PIG | O464271nb5 8pch
        CYTA_HUMAN | P010401cyu 1cyv 1dvc 1dvd 1gd3 1gd4 1n9j 1nb5 3k9m 3kfq 3kse

(-) Related Entries Specified in the PDB File

1nb5