Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  POTENT, NONPEPTIDE INHIBITORS OF HUMAN MAST CELL TRYPTASE
 
Authors :  J. C. Spurlino, F. Lewandowski, C. Milligan
Date :  08 Dec 07  (Deposition) - 09 Dec 08  (Release) - 09 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tryptase, Serine Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. J. Costanzo, S. C. Yabut, H. -C. Zhang, K. B. White, L. De Garavilla, Y. Wang, L. K. Minor, B. A. Tounge, A. N. Barnakov, F. Lewandowski, C. Milligan, J. C. Spurlino, W. M. Abraham, V. Boswell-Smith, C. P. Page, B. E. Maryanoff
Potent, Nonpeptide Inhibitors Of Human Mast Cell Tryptase. Synthesis And Biological Evaluation Of Novel Spirocyclic Piperidine Amide Derivatives
Bioorg. Med. Chem. Lett. V. 18 2114 2008
PubMed-ID: 18272363  |  Reference-DOI: 10.1016/J.BMCL.2008.01.093
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRYPTASE BETA 2
    ChainsA, B, C, D
    EC Number3.4.21.-
    EngineeredYES
    FragmentUNP RESIDUES 31-273
    GeneTPSB2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
111M4Ligand/Ion1-(1'-{[3-(METHYLSULFANYL)-2-BENZOTHIOPHEN-1-YL]CARBONYL}SPIRO[1-BENZOFURAN-3,4'-PIPERIDIN]-5-YL)METHANAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:87 , ASP A:188 , SER A:189 , CYS A:190 , GLN A:191 , SER A:194 , TRP A:214 , GLY A:215 , GLU A:216 , GLY A:217 , GLY A:225 , TYR C:84BINDING SITE FOR RESIDUE 11M A 244
2AC2SOFTWAREGLN B:87 , ASP B:188 , SER B:189 , CYS B:190 , GLN B:191 , SER B:194 , TRP B:214 , GLY B:215 , GLU B:216 , GLY B:217 , GLY B:225 , HOH B:290 , HOH B:297 , TYR D:84 , THR D:85BINDING SITE FOR RESIDUE 11M B 244
3AC3SOFTWARETYR B:84 , THR B:85 , GLN D:87 , ASP D:188 , SER D:189 , CYS D:190 , GLN D:191 , TRP D:214 , GLY D:215 , GLU D:216 , GLY D:217 , HOH D:302BINDING SITE FOR RESIDUE 11M D 244
4AC4SOFTWARETYR A:84 , THR A:85 , GLN C:87 , ASP C:188 , SER C:189 , CYS C:190 , GLN C:191 , SER C:194 , TRP C:214 , GLY C:215 , GLU C:216 , GLY C:217 , HOH C:303BINDING SITE FOR RESIDUE 11M C 244

(-) SS Bonds  (16, 16)

Asymmetric/Biological Unit
No.Residues
1A:29 -A:45
2A:125 -A:200
3A:158 -A:181
4A:190 -A:218
5B:29 -B:45
6B:125 -B:200
7B:158 -B:181
8B:190 -B:218
9C:29 -C:45
10C:125 -C:200
11C:158 -C:181
12C:190 -C:218
13D:29 -D:45
14D:125 -D:200
15D:158 -D:181
16D:190 -D:218

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Gly A:47 -Pro A:48
2Pro A:141 -Pro A:142
3Gly B:47 -Pro B:48
4Pro B:141 -Pro B:142
5Gly C:47 -Pro C:48
6Pro C:141 -Pro C:142
7Gly D:47 -Pro D:48
8Pro D:141 -Pro D:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (22, 88)

Asymmetric/Biological Unit (22, 88)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_064281H51RTRYB1_HUMANPolymorphism1060281A/B/C/DH21R
02UniProtVAR_064282G52DTRYB1_HUMANPolymorphism17841227A/B/C/DG22D
03UniProtVAR_064283P53RTRYB1_HUMANPolymorphism17841226A/B/C/DP23R
04UniProtVAR_064284V76LTRYB1_HUMANPolymorphism71384640A/B/C/DV46L
05UniProtVAR_014559A85TTRYB1_HUMANPolymorphism1141968A/B/C/DA55T
06UniProtVAR_064285T115ITRYB1_HUMANPolymorphism1064774A/B/C/DT85I
07UniProtVAR_064286A116ITRYB1_HUMANPolymorphism  ---A/B/C/DA86I
08UniProtVAR_064287I118TTRYB1_HUMANPolymorphism71376589A/B/C/DI88T
09UniProtVAR_016102N132KTRYB1_HUMANPolymorphism1800991A/B/C/DK102K
10UniProtVAR_064288V133ITRYB1_HUMANPolymorphism1064779A/B/C/DV103I
11UniProtVAR_051830H136RTRYB1_HUMANPolymorphism1064780A/B/C/DH106R
12UniProtVAR_014560T141ATRYB1_HUMANPolymorphism1800992A/B/C/DT111A
13UniProtVAR_064289T141MTRYB1_HUMANPolymorphism  ---A/B/C/DT111M
14UniProtVAR_014561D162NTRYB1_HUMANPolymorphism2234641A/B/C/DD132N
15UniProtVAR_064290R168PTRYB1_HUMANPolymorphism1141969A/B/C/DR138P
16UniProtVAR_014562P170STRYB1_HUMANPolymorphism2234904A/B/C/DP140S
17UniProtVAR_064291V205ITRYB1_HUMANPolymorphism1060284A/B/C/DV175I
18UniProtVAR_014563T215STRYB1_HUMANPolymorphism2234905A/B/C/DT185S
19UniProtVAR_014564R216QTRYB1_HUMANPolymorphism2234906A/B/C/DR186Q
20UniProtVAR_064292Q221KTRYB1_HUMANPolymorphism17841224A/B/C/DQ191K
21UniProtVAR_064293G245DTRYB1_HUMANPolymorphism1060292A/B/C/DG215D
22UniProtVAR_064294Y263NTRYB1_HUMANPolymorphism2234646A/B/C/DY233N

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

(-) PROSITE Motifs  (3, 12)

Asymmetric/Biological Unit (3, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.TRYB1_HUMAN31-272
 
 
 
  4A:1-242
B:1-242
C:1-242
D:1-242
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.TRYB1_HUMAN70-75
 
 
 
  4A:40-45
B:40-45
C:40-45
D:40-45
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.TRYB1_HUMAN218-229
 
 
 
  4A:188-199
B:188-199
C:188-199
D:188-199

(-) Exons   (4, 16)

Asymmetric/Biological Unit (4, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003388441bENSE00001748932chr16:1290697-129072933TRYB1_HUMAN-00--
1.1dENST000003388441dENSE00001591956chr16:1290940-129100061TRYB1_HUMAN1-21210--
1.2ENST000003388442ENSE00001631671chr16:1291154-1291325172TRYB1_HUMAN21-78584A:1-48
B:1-48
C:1-48
D:1-48
48
48
48
48
1.3aENST000003388443aENSE00001598761chr16:1291435-1291700266TRYB1_HUMAN78-167904A:48-137
B:48-137
C:48-137
D:48-137
90
90
90
90
1.4ENST000003388444ENSE00001679833chr16:1291828-1291991164TRYB1_HUMAN167-221554A:137-191
B:137-191
C:137-191
D:137-191
55
55
55
55
1.5bENST000003388445bENSE00001792150chr16:1292077-1292555479TRYB1_HUMAN222-275544A:192-243
B:192-243
C:192-243
D:192-243
52
52
52
52

(-) 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:243
 aligned with TRYB1_HUMAN | Q15661 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:243
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   
          TRYB1_HUMAN    31 IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVNVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPK 273
               SCOP domains d2zeba_ A: beta-Tryptase                                                                                                                                                                                                                            SCOP domains
               CATH domains 2zebA01     2zebA02 A:13-109,A:232-243 Trypsin-like serine proteases                                         2zebA01 A:1-12,A:110-231 Trypsin-like serine proteases                                                                    2zebA02      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee.....eeeeeeeeee..eeeehhhhhh....hhh.eeee..............eeeeee.............eeeee...........................eeeee................eeee..eehhhhhhhhhhh..............eeee..............eeeeee..eeeeeeeeee..........eeeee...hhhhhhh.... Sec.struct. author
             SAPs(SNPs) (1) --------------------RDR----------------------L--------T-----------------------------II-T-------------KI--R----A--------------------N-----P-S----------------------------------I---------SQ----K-----------------------D-----------------N---------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------M------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                PROSITE (1) TRYPSIN_DOM  PDB: A:1-242 UniProt: 31-272                                                                                                                                                                                                         - PROSITE (1)
                PROSITE (2) ---------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:1-48 UniProt: 21-78            ----------------------------------------------------------------------------------------Exon 1.4  PDB: A:137-191 UniProt: 167-221              Exon 1.5b  PDB: A:192-243 UniProt: 222-275           Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.3a  PDB: A:48-137 UniProt: 78-167                                                  ---------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2zeb A   1 IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVKVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPK 243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   

Chain B from PDB  Type:PROTEIN  Length:243
 aligned with TRYB1_HUMAN | Q15661 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:243
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   
          TRYB1_HUMAN    31 IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVNVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPK 273
               SCOP domains d2zebb_ B: beta-Tryptase                                                                                                                                                                                                                            SCOP domains
               CATH domains 2zebB01     2zebB02 B:13-109,B:232-243 Trypsin-like serine proteases                                         2zebB01 B:1-12,B:110-231 Trypsin-like serine proteases                                                                    2zebB02      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee.....eeeeeeeeee..eeeehhhhh.....hhh.eeee............eeeeeeee.............eeeee...........................eeeee................eeee..eehhhhhhhhhhh..............eeee..............eeeeee..eeeeeeeeee..........eeeee...hhhhhhh.... Sec.struct. author
             SAPs(SNPs) (1) --------------------RDR----------------------L--------T-----------------------------II-T-------------KI--R----A--------------------N-----P-S----------------------------------I---------SQ----K-----------------------D-----------------N---------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------M------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                PROSITE (1) TRYPSIN_DOM  PDB: B:1-242 UniProt: 31-272                                                                                                                                                                                                         - PROSITE (1)
                PROSITE (2) ---------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: B:1-48 UniProt: 21-78            ----------------------------------------------------------------------------------------Exon 1.4  PDB: B:137-191 UniProt: 167-221              Exon 1.5b  PDB: B:192-243 UniProt: 222-275           Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.3a  PDB: B:48-137 UniProt: 78-167                                                  ---------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2zeb B   1 IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVKVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPK 243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   

Chain C from PDB  Type:PROTEIN  Length:243
 aligned with TRYB1_HUMAN | Q15661 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:243
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   
          TRYB1_HUMAN    31 IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVNVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPK 273
               SCOP domains d2zebc_ C: beta-Tryptase                                                                                                                                                                                                                            SCOP domains
               CATH domains 2zebC01     2zebC02 C:13-109,C:232-243 Trypsin-like serine proteases                                         2zebC01 C:1-12,C:110-231 Trypsin-like serine proteases                                                                    2zebC02      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee.....eeeeeeeeee..eeeehhhhh.....hhh.eeeee.............eeeeee.............eeeee...........................eeeee................eeee..eehhhhhhhhhhh..............eeee..............eeeee....eeeeeeeee..........eeeee...hhhhhhh.... Sec.struct. author
             SAPs(SNPs) (1) --------------------RDR----------------------L--------T-----------------------------II-T-------------KI--R----A--------------------N-----P-S----------------------------------I---------SQ----K-----------------------D-----------------N---------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------M------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                PROSITE (1) TRYPSIN_DOM  PDB: C:1-242 UniProt: 31-272                                                                                                                                                                                                         - PROSITE (1)
                PROSITE (2) ---------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: C:1-48 UniProt: 21-78            ----------------------------------------------------------------------------------------Exon 1.4  PDB: C:137-191 UniProt: 167-221              Exon 1.5b  PDB: C:192-243 UniProt: 222-275           Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.3a  PDB: C:48-137 UniProt: 78-167                                                  ---------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2zeb C   1 IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVKVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPK 243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   

Chain D from PDB  Type:PROTEIN  Length:243
 aligned with TRYB1_HUMAN | Q15661 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:243
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   
          TRYB1_HUMAN    31 IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVNVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPK 273
               SCOP domains d2zebd_ D: beta-Tryptase                                                                                                                                                                                                                            SCOP domains
               CATH domains 2zebD01     2zebD02 D:13-109,D:232-243 Trypsin-like serine proteases                                         2zebD01 D:1-12,D:110-231 Trypsin-like serine proteases                                                                    2zebD02      CATH domains
           Pfam domains (1) Trypsin-2zebD01 D:1-237                                                                                                                                                                                                                      ------ Pfam domains (1)
           Pfam domains (2) Trypsin-2zebD02 D:1-237                                                                                                                                                                                                                      ------ Pfam domains (2)
           Pfam domains (3) Trypsin-2zebD03 D:1-237                                                                                                                                                                                                                      ------ Pfam domains (3)
           Pfam domains (4) Trypsin-2zebD04 D:1-237                                                                                                                                                                                                                      ------ Pfam domains (4)
         Sec.struct. author ....ee........eeeeee.....eeeeeeeeee..eeeehhhhh.....hhh.eeee............eeeeeeee.............eeeee...........................eeeee................eeee..eehhhhhhhhhhh..............eeee..............eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhh.. Sec.struct. author
             SAPs(SNPs) (1) --------------------RDR----------------------L--------T-----------------------------II-T-------------KI--R----A--------------------N-----P-S----------------------------------I---------SQ----K-----------------------D-----------------N---------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------M------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                PROSITE (1) TRYPSIN_DOM  PDB: D:1-242 UniProt: 31-272                                                                                                                                                                                                         - PROSITE (1)
                PROSITE (2) ---------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: D:1-48 UniProt: 21-78            ----------------------------------------------------------------------------------------Exon 1.4  PDB: D:137-191 UniProt: 167-221              Exon 1.5b  PDB: D:192-243 UniProt: 222-275           Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.3a  PDB: D:48-137 UniProt: 78-167                                                  ---------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2zeb D   1 IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVKVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPK 243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   

   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, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 8)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)
1a2zebA02A:13-109,A:232-243
1b2zebA01A:1-12,A:110-231
1c2zebB01B:1-12,B:110-231
1d2zebC01C:1-12,C:110-231
1e2zebD01D:1-12,D:110-231
1f2zebB02B:13-109,B:232-243
1g2zebC02C:13-109,C:232-243
1h2zebD02D:13-109,D:232-243

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (TRYB1_HUMAN | Q15661)
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:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    11M  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:47 - Pro A:48   [ RasMol ]  
    Gly B:47 - Pro B:48   [ RasMol ]  
    Gly C:47 - Pro C:48   [ RasMol ]  
    Gly D:47 - Pro D:48   [ RasMol ]  
    Pro A:141 - Pro A:142   [ RasMol ]  
    Pro B:141 - Pro B:142   [ RasMol ]  
    Pro C:141 - Pro C:142   [ RasMol ]  
    Pro D:141 - Pro D:142   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2zeb
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TRYB1_HUMAN | Q15661
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.21.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  TRYB1_HUMAN | Q15661
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TRYB1_HUMAN | Q156611lto 2f9n 2f9o 2f9p 2za5 2zec 4a6l 4mpu 4mpv 4mpw 4mpx 4mqa 5f03

(-) Related Entries Specified in the PDB File

2zec