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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN GRANZYME B
 
Authors :  E. Estebanez-Perpina, P. Fuentes-Prior, D. Belorgey, H. Rubin, W. Bod
Date :  03 Sep 00  (Deposition) - 31 Jan 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Chymotrypsin-Like Serine Proteinase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Estebanez-Perpina, P. Fuentes-Prior, D. Belorgey, M. Braun, R. Kiefersauer, K. Maskos, R. Huber, H. Rubin, W. Bode
Crystal Structure Of The Caspase Activator Human Granzyme B A Proteinase Highly Specific For An Asp-P1 Residue.
Biol. Chem. V. 381 1203 2000
PubMed-ID: 11209755  |  Reference-DOI: 10.1515/BC.2000.148

(-) Compounds

Molecule 1 - GRANZYME B
    ChainsA, B
    EC Number3.4.21.79
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS SYSTEM
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
3NDG2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
4SO42Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:34 , ASN A:65 , PHE A:82 , NAG A:601 , TRP B:36 , SER B:63 , NDG B:700 , NAG B:701BINDING SITE FOR RESIDUE NDG A 600
2AC2SOFTWARENDG A:600 , BMA A:602 , TRP B:36 , NDG B:700 , NAG B:701BINDING SITE FOR RESIDUE NAG A 601
3AC3SOFTWARENAG A:601BINDING SITE FOR RESIDUE BMA A 602
4AC4SOFTWARENDG A:600 , NAG A:601 , MET B:34 , SER B:63 , ASN B:65 , PHE B:82 , NAG B:701BINDING SITE FOR RESIDUE NDG B 700
5AC5SOFTWAREGLU A:109 , ARG A:110 , NDG A:600 , NAG A:601 , NDG B:700 , BMA B:702BINDING SITE FOR RESIDUE NAG B 701
6AC6SOFTWARENAG B:701BINDING SITE FOR RESIDUE BMA B 702
7AC7SOFTWAREHIS A:57 , LYS A:192 , GLY A:193 , SER A:195BINDING SITE FOR RESIDUE SO4 A 800
8AC8SOFTWARELYS B:192 , SER B:195BINDING SITE FOR RESIDUE SO4 B 900

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:58
2A:136 -A:201
3A:168 -A:182
4B:42 -B:58
5B:136 -B:201
6B:168 -B:182

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:224A-Pro A:225
2Pro B:224A-Pro B:225

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric/Biological Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_018371R55QGRAB_HUMANPolymorphism8192917A/BQ48Q
2UniProtVAR_047409P94AGRAB_HUMANPolymorphism11539752A/BP88A
3UniProtVAR_018381Y247HGRAB_HUMANPolymorphism2236338A/BY245H

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

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.GRAB_HUMAN21-245
 
  2A:16-243
B:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.GRAB_HUMAN60-65
 
  2A:53-58
B:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.GRAB_HUMAN197-208
 
  2A:189-200
B:189-200

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002163411aENSE00001267008chr14:25103473-25103312162GRAB_HUMAN1-19190--
1.3bENST000002163413bENSE00000654543chr14:25102268-25102121148GRAB_HUMAN19-68502A:16-61
B:16-61
48
48
1.5ENST000002163415ENSE00001762893chr14:25101665-25101530136GRAB_HUMAN68-113462A:61-107 (gaps)
B:61-107 (gaps)
47
47
1.6bENST000002163416bENSE00000654540chr14:25101324-25101064261GRAB_HUMAN114-200872A:108-192 (gaps)
B:108-192 (gaps)
88
88
1.7dENST000002163417dENSE00001929764chr14:25100420-25100161260GRAB_HUMAN201-247472A:193-245 (gaps)
B:193-245 (gaps)
54
54

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:227
 aligned with GRAB_HUMAN | P10144 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:227
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       
          GRAB_HUMAN     21 IIGGHEAKPHSRPYMAYLMIWDQKSLKRCGGFLIRDDFVLTAAHCWGSSINVTLGAHNIKEQEPTQQFIPVKRPIPHPAYNPKNFSNDIMLLQLERKAKRTRAVQPLRLPSNKAQVKPGQTCSVAGWGQTAPLGKHSHTLQEVKMTVQEDRKCESDLRHYYDSTIELCVGDPEIKKTSFKGDSGGPLVCNKVAQGIVSYGRNNGMPPRACTKVSSFVHWIKKTMKRY  247
               SCOP domains d1fq3a_ A: Granzyme B                                                                                                                                                                                                               SCOP domains
               CATH domains 1fq3A01     1fq3A02 A:28-120,A:233-244 Trypsin-like serine proteases                                      1fq3A01 A:16-27,A:121-232 Trypsin-like serine proteases                                                     1fq3A02     - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee..eee..eee..eeeeee..eeeehhhhh..eeeeee............eeeeeeee...............eeeee..........................eee....................eee..hhhhhh...........ee............................ee............eehhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------Q--------------------------------------A--------------------------------------------------------------------------------------------------------------------------------------------------------H SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 21-245                                                                                                                                                                                       -- PROSITE (1)
                PROSITE (2) ---------------------------------------TRYPSI-----------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.3b  PDB: A:16-61 UniProt: 19-68          ---------------------------------------------Exon 1.6b  PDB: A:108-192 (gaps) UniProt: 114-200                                      Exon 1.7d  PDB: A:193-245 (gaps)                Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.5  PDB: A:61-107 (gaps) UniProt: 68-113-------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                1fq3 A   16 IIGGHEAKPHSRPYMAYLMIWDQKSLKRCGGFLIQDDFVLTAAHCWGSSINVTLGAHNIKEQEPTQQFIPVKRPIPHPAYNPKNFSNDIMLLQLERKAKRTRAVQPLRLPSNKAQVKPGQTCSVAGWGQTAPLGKHSHTLQEVKMTVQEDRKCESDLRHYYDSTIELCVGDPEIKKTSFKGDSGGPLVCNKVAQGIVSYGRNNGMPPRACTKVSSFVHWIKKTMKRY  245
                                    25        35  ||    43        53       |64        74        84        94       104       114       124       134       144    || 155       165     | 174       184|    | 192      202A||     216   ||| 228       238       
                                                37A|                      61|                                                                                   149|                170A           184A 188A          202A||         220||                     
                                                 37B                       63                                                                                    151                                                    203|          224|                     
                                                                                                                                                                                                                         208          224A                     

Chain B from PDB  Type:PROTEIN  Length:227
 aligned with GRAB_HUMAN | P10144 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:227
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       
          GRAB_HUMAN     21 IIGGHEAKPHSRPYMAYLMIWDQKSLKRCGGFLIRDDFVLTAAHCWGSSINVTLGAHNIKEQEPTQQFIPVKRPIPHPAYNPKNFSNDIMLLQLERKAKRTRAVQPLRLPSNKAQVKPGQTCSVAGWGQTAPLGKHSHTLQEVKMTVQEDRKCESDLRHYYDSTIELCVGDPEIKKTSFKGDSGGPLVCNKVAQGIVSYGRNNGMPPRACTKVSSFVHWIKKTMKRY  247
               SCOP domains d1fq3b_ B: Granzyme B                                                                                                                                                                                                               SCOP domains
               CATH domains 1fq3B01     1fq3B02 B:28-120,B:233-244 Trypsin-like serine proteases                                      1fq3B01 B:16-27,B:121-232 Trypsin-like serine proteases                                                     1fq3B02     - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee....eeeeeeeeee..eeeehhhhh...eeeee............eeeeeeee...............eeeee..........................eeee...................eee..hhhhhhhhh........ee..................eee....eeeeeee.........eeehhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------Q--------------------------------------A--------------------------------------------------------------------------------------------------------------------------------------------------------H SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:16-243 UniProt: 21-245                                                                                                                                                                                       -- PROSITE (1)
                PROSITE (2) ---------------------------------------TRYPSI-----------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.3b  PDB: B:16-61 UniProt: 19-68          ---------------------------------------------Exon 1.6b  PDB: B:108-192 (gaps) UniProt: 114-200                                      Exon 1.7d  PDB: B:193-245 (gaps)                Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.5  PDB: B:61-107 (gaps) UniProt: 68-113-------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                1fq3 B   16 IIGGHEAKPHSRPYMAYLMIWDQKSLKRCGGFLIQDDFVLTAAHCWGSSINVTLGAHNIKEQEPTQQFIPVKRPIPHPAYNPKNFSNDIMLLQLERKAKRTRAVQPLRLPSNKAQVKPGQTCSVAGWGQTAPLGKHSHTLQEVKMTVQEDRKCESDLRHYYDSTIELCVGDPEIKKTSFKGDSGGPLVCNKVAQGIVSYGRNNGMPPRACTKVSSFVHWIKKTMKRY  245
                                    25        35  ||    43        53       |64        74        84        94       104       114       124       134       144    || 155       165     | 174       184|    | 192       202||     216   ||| 228       238       
                                                37A|                      61|                                                                                   149|                170A           184A 188A            203|         220||                     
                                                 37B                       63                                                                                    151                                                     208          224|                     
                                                                                                                                                                                                                                      224A                     

   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/Biological Unit

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)
1a1fq3A01A:16-27,A:121-232
1b1fq3B01B:16-27,B:121-232
1c1fq3A02A:28-120,A:233-244
1d1fq3B02B:28-120,B:233-244

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FQ3)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GRAB_HUMAN | P10144)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0042267    natural killer cell mediated cytotoxicity    The directed killing of a target cell by a natural killer cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors.
    GO:1900740    positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway.
    GO:0016485    protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0001772    immunological synapse    An area of close contact between a lymphocyte (T-, B-, or natural killer cell) and a target cell formed through the clustering of particular signaling and adhesion molecules and their associated membrane rafts on both the lymphocyte and the target cell and facilitating activation of the lymphocyte, transfer of membrane from the target cell to the lymphocyte, and in some situations killing of the target cell through release of secretory granules and/or death-pathway ligand-receptor interaction.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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
        GRAB_HUMAN | P101441iau

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1FQ3)