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(-) Description

Title :  CRYSTAL STRUCTURE OF THROMBIN BOUND TO THE ACTIVATION DOMAIN QEDQVDPRLIDGKMTRRGDS OF PROTEIN C
 
Authors :  N. Pozzi, S. Barranco-Medina, Z. Chen, E. Di Cera
Date :  20 Feb 12  (Deposition) - 09 May 12  (Release) - 15 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E  (1x)
Biol. Unit 2:  C,D,F  (1x)
Keywords :  Serine Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Pozzi, S. Barranco-Medina, Z. Chen, E. Di Cera
Exposure Of R169 Controls Protein C Activation And Autoactivation.
Blood V. 120 664 2012
PubMed-ID: 22535660  |  Reference-DOI: 10.1182/BLOOD-2012-03-415323
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THROMBIN LIGHT CHAIN
    ChainsA, C
    EC Number3.4.21.5
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneF2, HUMAN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - THROMBIN HEAVY CHAIN
    ChainsB, D
    EC Number3.4.21.5
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneF2, HUMAN
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - VITAMIN K-DEPENDENT PROTEIN C
    ChainsE, F
    EC Number3.4.21.69
    EngineeredYES
    FragmentUNP RESIDUES 204-223
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymANTICOAGULANT PROTEIN C, AUTOPROTHROMBIN IIA, BLOOD COAGULATION FACTOR XIV, VITAMIN K-DEPENDENT PROTEIN C LIGHT CHAIN, VITAMIN K-DEPENDENT PROTEIN C HEAVY CHAIN, ACTIVATION PEPTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)AB  E 
Biological Unit 2 (1x)  CD F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2NA2Ligand/IonSODIUM ION
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2NA-1Ligand/IonSODIUM ION
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2NA-1Ligand/IonSODIUM ION
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:221A , LYS B:224 , HOH B:512 , HOH B:538 , HOH B:544 , HOH B:564BINDING SITE FOR RESIDUE NA B 401
2AC2SOFTWAREALA B:113 , PHE B:114 , LYS B:169 , THR B:172 , ILE B:174 , ARG B:175 , ILE B:176BINDING SITE FOR RESIDUE PEG B 402
3AC3SOFTWAREASP B:21 , PRO B:152 , SER B:153 , HOH B:623 , GLN D:151BINDING SITE FOR RESIDUE ACT B 403
4AC4SOFTWAREVAL D:163 , ARG D:165 , HOH D:514 , HOH D:515BINDING SITE FOR RESIDUE ACT D 301
5AC5SOFTWAREARG D:221A , LYS D:224 , HOH D:415 , HOH D:424 , HOH D:446 , HOH D:461BINDING SITE FOR RESIDUE NA D 302

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:1 -B:122
2B:42 -B:58
3B:168 -B:182
4B:191 -B:220
5C:1 -D:122
6D:42 -D:58
7D:168 -D:182
8D:191 -D:220

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser B:36A-Pro B:37
2Ser D:36A-Pro D:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (11, 22)

Asymmetric Unit (11, 22)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_006714M380TTHRB_HUMANDisease (FA2D)121918481B/DM32T
02UniProtVAR_011782P386TTHRB_HUMANPolymorphism5897B/DP37T
03UniProtVAR_006664P210LPROC_HUMANDisease (THPH3)121918145E/FP40L
04UniProtVAR_006666R211QPROC_HUMANPolymorphism28933987E/FR41Q
05UniProtVAR_006665R211WPROC_HUMANDisease (THPH3)28933986E/FR41W
06UniProtVAR_006715R425CTHRB_HUMANDisease (FA2D)121918479B/DR67C
07UniProtVAR_006716R431HTHRB_HUMANDisease (FA2D)121918482B/DR73H
08UniProtVAR_006717R461WTHRB_HUMANDisease (FA2D)121918478B/DR101W
09UniProtVAR_006718E509ATHRB_HUMANDisease (FA2D)  ---B/DE146A
10UniProtVAR_068913E532QTHRB_HUMANPolymorphism  ---B/DE164Q
11UniProtVAR_006719G601VTHRB_HUMANDisease (FA2D)121918480B/DG226V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (11, 11)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_006714M380TTHRB_HUMANDisease (FA2D)121918481BM32T
02UniProtVAR_011782P386TTHRB_HUMANPolymorphism5897BP37T
03UniProtVAR_006664P210LPROC_HUMANDisease (THPH3)121918145EP40L
04UniProtVAR_006666R211QPROC_HUMANPolymorphism28933987ER41Q
05UniProtVAR_006665R211WPROC_HUMANDisease (THPH3)28933986ER41W
06UniProtVAR_006715R425CTHRB_HUMANDisease (FA2D)121918479BR67C
07UniProtVAR_006716R431HTHRB_HUMANDisease (FA2D)121918482BR73H
08UniProtVAR_006717R461WTHRB_HUMANDisease (FA2D)121918478BR101W
09UniProtVAR_006718E509ATHRB_HUMANDisease (FA2D)  ---BE146A
10UniProtVAR_068913E532QTHRB_HUMANPolymorphism  ---BE164Q
11UniProtVAR_006719G601VTHRB_HUMANDisease (FA2D)121918480BG226V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (11, 11)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_006714M380TTHRB_HUMANDisease (FA2D)121918481DM32T
02UniProtVAR_011782P386TTHRB_HUMANPolymorphism5897DP37T
03UniProtVAR_006664P210LPROC_HUMANDisease (THPH3)121918145FP40L
04UniProtVAR_006666R211QPROC_HUMANPolymorphism28933987FR41Q
05UniProtVAR_006665R211WPROC_HUMANDisease (THPH3)28933986FR41W
06UniProtVAR_006715R425CTHRB_HUMANDisease (FA2D)121918479DR67C
07UniProtVAR_006716R431HTHRB_HUMANDisease (FA2D)121918482DR73H
08UniProtVAR_006717R461WTHRB_HUMANDisease (FA2D)121918478DR101W
09UniProtVAR_006718E509ATHRB_HUMANDisease (FA2D)  ---DE146A
10UniProtVAR_068913E532QTHRB_HUMANPolymorphism  ---DE164Q
11UniProtVAR_006719G601VTHRB_HUMANDisease (FA2D)121918480DG226V

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

(-) PROSITE Motifs  (3, 7)

Asymmetric Unit (3, 7)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.PROC_HUMAN212-450  1F:42-42
THRB_HUMAN364-618
 
  2B:16-243
D:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.THRB_HUMAN402-407
 
  2B:53-58
D:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.THRB_HUMAN562-573
 
  2B:189-200
D:189-200
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.PROC_HUMAN212-450  0-
THRB_HUMAN364-618
 
  1B:16-243
-
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.THRB_HUMAN402-407
 
  1B:53-58
-
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.THRB_HUMAN562-573
 
  1B:189-200
-
Biological Unit 2 (3, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.PROC_HUMAN212-450  1F:42-42
THRB_HUMAN364-618
 
  1-
D:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.THRB_HUMAN402-407
 
  1-
D:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.THRB_HUMAN562-573
 
  1-
D:189-200

(-) Exons   (8, 18)

Asymmetric Unit (8, 18)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002340711aENSE00001747079chr2:128176003-12817606866PROC_HUMAN-00--
1.2eENST000002340712eENSE00000857263chr2:128177498-12817758891PROC_HUMAN1-24240--
1.3aENST000002340713aENSE00001019166chr2:128178859-128179025167PROC_HUMAN24-79560--
1.4aENST000002340714aENSE00001657237chr2:128180493-12818051725PROC_HUMAN80-8890--
1.4hENST000002340714hENSE00000775732chr2:128180610-128180747138PROC_HUMAN88-134470--
1.4kENST000002340714kENSE00001019181chr2:128180850-128180984135PROC_HUMAN134-179460--
1.5bENST000002340715bENSE00000775730chr2:128183661-128183803143PROC_HUMAN179-226482E:34-41
F:34-42
8
9
1.6ENST000002340716ENSE00000775729chr2:128184681-128184798118PROC_HUMAN227-266400--
1.7dENST000002340717dENSE00001853552chr2:128185933-128186822890PROC_HUMAN266-4611960--

2.1aENST000003119071aENSE00001931088chr11:46740730-46740864135THRB_HUMAN1-27270--
2.2aENST000003119072aENSE00001181543chr11:46741252-46741412161THRB_HUMAN27-80540--
2.3ENST000003119073ENSE00001181538chr11:46742073-4674209725THRB_HUMAN81-8990--
2.4ENST000003119074ENSE00001181532chr11:46742340-4674239051THRB_HUMAN89-106180--
2.6aENST000003119076aENSE00001181527chr11:46744730-46744835106THRB_HUMAN106-141360--
2.6cENST000003119076cENSE00001181524chr11:46744932-46745068137THRB_HUMAN141-187470--
2.7bENST000003119077bENSE00001688723chr11:46747409-46747723315THRB_HUMAN187-2921060--
2.8ENST000003119078ENSE00002179953chr11:46748048-46748176129THRB_HUMAN292-335442A:1D-1A
-
C:1D-1A
-
4
-
4
-
2.9ENST000003119079ENSE00001770269chr11:46748261-46748387127THRB_HUMAN335-377434A:1A-15
B:16-29
C:1A-15
D:16-29
29
14
29
14
2.10ENST0000031190710ENSE00001650441chr11:46749546-46749713168THRB_HUMAN377-433572-
B:29-75
-
D:29-75
-
57
-
57
2.11bENST0000031190711bENSE00001657931chr11:46750214-46750387174THRB_HUMAN433-491592-
B:75-129B
-
D:75-129B
-
59
-
59
2.12ENST0000031190712ENSE00001646362chr11:46750930-46751111182THRB_HUMAN491-552622-
B:129B-184 (gaps)
-
D:129B-184 (gaps)
-
62
-
62
2.13ENST0000031190713ENSE00001680217chr11:46760598-4676066871THRB_HUMAN552-575242-
B:184-202
-
D:184-202
-
24
-
24
2.14cENST0000031190714cENSE00001227030chr11:46760815-46761056242THRB_HUMAN576-622472-
B:203-246 (gaps)
-
D:203-247 (gaps)
-
47
-
48

(-) 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:32
 aligned with THRB_HUMAN | P00734 from UniProtKB/Swiss-Prot  Length:622

    Alignment length:32
                                   341       351       361  
          THRB_HUMAN    332 GEADCGLRPLFEKKSLEDKTERELLESYIDGR  363
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------- PROSITE (3)
                PROSITE (1) -------------------------------- PROSITE (1)
           Transcript 2 (1) 2.8 ---------------------------- Transcript 2 (1)
           Transcript 2 (2) ---Exon 2.9  PDB: A:1A-15        Transcript 2 (2)
                4dt7 A   1D GEADCGLRPLFEKKSLEDKTERELLESYIDGR   15
                            ||||     6       14B|||||||14L| 
                           1D|||            14A||||||14J||| 
                            1C||             14B||||||14K|| 
                             1B|              14C||||||14L| 
                              1A               14D||||| 14M 
                                                14E||||     
                                                 14F|||     
                                                  14G||     
                                                   14H|     
                                                    14I     

Chain B from PDB  Type:PROTEIN  Length:252
 aligned with THRB_HUMAN | P00734 from UniProtKB/Swiss-Prot  Length:622

    Alignment length:258
                                   373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613        
          THRB_HUMAN    364 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG  621
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee........eeeeee....eeeeeeee....eeeehhhhheehhhhee.hhhh.eeee.............eeeeeeeeee..............eeeee................hhhhhhhhh....eeeeee........------......eeeeee..hhhhhhhh........eeee..hhhhh............eeeee......eeeeeeeeee.........eeeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------T-----T--------------------------------------C-----H-----------------------------W-----------------------------------------------A----------------------Q--------------------------------------------------------------------V-------------------- SAPs(SNPs)
                PROSITE (2) TRYPSIN_DOM  PDB: B:16-243 UniProt: 364-618                                                                                                                                                                                                                    --- PROSITE (2)
                PROSITE (3) --------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------------ PROSITE (1)
           Transcript 2 (1) -------------Exon 2.10  PDB: B:29-75 UniProt: 377-433                 ---------------------------------------------------------Exon 2.12  PDB: B:129B-184 (gaps) UniProt: 491-552            -----------------------Exon 2.14c  PDB: B:203-246 (gaps)              Transcript 2 (1)
           Transcript 2 (2) Exon 2.9      -------------------------------------------------------Exon 2.11b  PDB: B:75-129B UniProt: 433-491                ------------------------------------------------------------Exon 2.13  PDB: B:184-20---------------------------------------------- Transcript 2 (2)
                4dt7 B   16 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETW------GQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDAGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG  246
                                    25        35 |      44        54      |60D|||||   65        75  |     84        94   |   103       113       123      |130       140       | -    |  155       165       175      184A  |||| 190       200    || 208       219  |    228       238        
                                               36A                      60A||||||||               77A                  97A                             129A||                148    150                               184A  ||||               204A|          217|  |                         
                                                                         60B|||||||                                                                     129B|                                                            186A|||                204B           219  |                         
                                                                          60C||||||                                                                      129C                                                             186B||                                 221A                         
                                                                           60D|||||                                                                                                                                        186C|                                                              
                                                                            60E||||                                                                                                                                         186D                                                              
                                                                             60F|||                                                                                                                                                                                                           
                                                                              60G||                                                                                                                                                                                                           
                                                                               60H|                                                                                                                                                                                                           
                                                                                60I                                                                                                                                                                                                           

Chain C from PDB  Type:PROTEIN  Length:32
 aligned with THRB_HUMAN | P00734 from UniProtKB/Swiss-Prot  Length:622

    Alignment length:32
                                   341       351       361  
          THRB_HUMAN    332 GEADCGLRPLFEKKSLEDKTERELLESYIDGR  363
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------- PROSITE (3)
                PROSITE (1) -------------------------------- PROSITE (1)
           Transcript 2 (1) 2.8 ---------------------------- Transcript 2 (1)
           Transcript 2 (2) ---Exon 2.9  PDB: C:1A-15        Transcript 2 (2)
                4dt7 C   1D GEADCGLRPLFEKKSLEDKTERELLESYIDGR   15
                            ||||     6       14B|||||||14L| 
                           1D|||            14A||||||14J||| 
                            1C||             14B||||||14K|| 
                             1B|              14C||||||14L| 
                              1A               14D||||| 14M 
                                                14E||||     
                                                 14F|||     
                                                  14G||     
                                                   14H|     
                                                    14I     

Chain D from PDB  Type:PROTEIN  Length:253
 aligned with THRB_HUMAN | P00734 from UniProtKB/Swiss-Prot  Length:622

    Alignment length:259
                                   373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613         
          THRB_HUMAN    364 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE  622
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee....eeeeeeee....eeeehhhh.eehhhhee.hhh.eeeee.............eee.eeeeee..............eeeee................hhhhhhhhh....eeeeee........------......eeeeee..hhhhhhhh........eeee..hhhhh............eeeee......eeeeeeeeee.........eeeee...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------T-----T--------------------------------------C-----H-----------------------------W-----------------------------------------------A----------------------Q--------------------------------------------------------------------V--------------------- SAPs(SNPs)
                PROSITE (2) TRYPSIN_DOM  PDB: D:16-243 UniProt: 364-618                                                                                                                                                                                                                    ---- PROSITE (2)
                PROSITE (3) --------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------------- PROSITE (1)
           Transcript 2 (1) -------------Exon 2.10  PDB: D:29-75 UniProt: 377-433                 ---------------------------------------------------------Exon 2.12  PDB: D:129B-184 (gaps) UniProt: 491-552            -----------------------Exon 2.14c  PDB: D:203-247 (gaps)               Transcript 2 (1)
           Transcript 2 (2) Exon 2.9      -------------------------------------------------------Exon 2.11b  PDB: D:75-129B UniProt: 433-491                ------------------------------------------------------------Exon 2.13  PDB: D:184-20----------------------------------------------- Transcript 2 (2)
                4dt7 D   16 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETW------GQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDAGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE  247
                                    25        35 |      44        54      |60D|||||   65        75  |     84        94   |   103       113       123      |130       140       | -    |  155       165       175      184A  |||| 190       200    || 208       219  |    228       238         
                                               36A                      60A||||||||               77A                  97A                             129A||                148    150                               184A  ||||               204A|          217|  |                          
                                                                         60B|||||||                                                                     129B|                                                            186A|||                204B           219  |                          
                                                                          60C||||||                                                                      129C                                                             186B||                                 221A                          
                                                                           60D|||||                                                                                                                                        186C|                                                               
                                                                            60E||||                                                                                                                                         186D                                                               
                                                                             60F|||                                                                                                                                                                                                            
                                                                              60G||                                                                                                                                                                                                            
                                                                               60H|                                                                                                                                                                                                            
                                                                                60I                                                                                                                                                                                                            

Chain E from PDB  Type:PROTEIN  Length:8
 aligned with PROC_HUMAN | P04070 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:8
          PROC_HUMAN    204 QEDQVDPR  211
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author .....ee. Sec.struct. author
             SAPs(SNPs) (1) ------LQ SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------W SAPs(SNPs) (2)
                    PROSITE -------- PROSITE
               Transcript 1 1.5b     Transcript 1
                4dt7 E   34 QEDQVDPR   41

Chain F from PDB  Type:PROTEIN  Length:9
 aligned with PROC_HUMAN | P04070 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:9
          PROC_HUMAN    204 QEDQVDPRL  212
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author .....ee.. Sec.struct. author
             SAPs(SNPs) (1) ------LQ- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------W- SAPs(SNPs) (2)
                    PROSITE --------T PROSITE
               Transcript 1 Exon 1.5b Transcript 1
                4dt7 F   34 QEDQVDPRL   42

   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  (0, 0)

(no "SCOP Domain" information available for 4DT7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DT7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DT7)

(-) Gene Ontology  (58, 75)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (THRB_HUMAN | P00734)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
    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:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    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).
    GO:0070053    thrombospondin receptor activity    Combining with thrombospondin and transmitting the signal to initiate a change in cell activity.
biological process
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0006953    acute-phase response    An acute inflammatory response that involves non-antibody proteins whose concentrations in the plasma increase in response to infection or injury of homeothermic animals.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0007597    blood coagulation, intrinsic pathway    A protein activation cascade that contributes to blood coagulation and consists of the interactions among high molecular weight kininogen, prekallikrein, and factor XII that lead to the activation of clotting factor X.
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0071260    cellular response to mechanical stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
    GO:0042730    fibrinolysis    A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0048712    negative regulation of astrocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of astrocyte differentiation.
    GO:0051918    negative regulation of fibrinolysis    Any process that stops, prevents, or reduces the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots.
    GO:0010544    negative regulation of platelet activation    Any process that decreases the rate or frequency of platelet activation. Platelet activation is a series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue.
    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:0017187    peptidyl-glutamic acid carboxylation    The gamma-carboxylation of peptidyl-glutamic acid; catalyzed by the vitamin K dependent gamma-glutamyl carboxylase.
    GO:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    GO:0030194    positive regulation of blood coagulation    Any process that activates or increases the frequency, rate or extent of blood coagulation.
    GO:0030307    positive regulation of cell growth    Any process that activates or increases the frequency, rate, extent or direction of cell growth.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0032967    positive regulation of collagen biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
    GO:0014068    positive regulation of phosphatidylinositol 3-kinase signaling    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    GO:1900738    positive regulation of phospholipase C-activating G-protein coupled receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of phospholipase C-activating G-protein coupled receptor signaling pathway.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:2000379    positive regulation of reactive oxygen species metabolic process    Any process that activates or increases the frequency, rate or extent of reactive oxygen species metabolic process.
    GO:0051281    positive regulation of release of sequestered calcium ion into cytosol    Any process that activates or increases the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0030193    regulation of blood coagulation    Any process that modulates the frequency, rate or extent of blood coagulation.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0051480    regulation of cytosolic calcium ion concentration    Any process involved in the maintenance of an internal steady state of calcium ions within the cytosol of a cell or between the cytosol and its surroundings.
    GO:0010468    regulation of gene expression    Any process that modulates 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:0014854    response to inactivity    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 an inactivity stimulus.
    GO:0009611    response to wounding    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
    GO:0006465    signal peptide processing    The proteolytic removal of a signal peptide from a protein during or after transport to a specific location in the cell.
cellular component
    GO:0005796    Golgi lumen    The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    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: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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain E,F   (PROC_HUMAN | P04070)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    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:0030195    negative regulation of blood coagulation    Any process that stops, prevents, or reduces the frequency, rate or extent of blood coagulation.
    GO:0050819    negative regulation of coagulation    Any process that stops, prevents, or reduces the frequency, rate or extent of coagulation.
    GO:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:0017187    peptidyl-glutamic acid carboxylation    The gamma-carboxylation of peptidyl-glutamic acid; catalyzed by the vitamin K dependent gamma-glutamyl carboxylase.
    GO:1903142    positive regulation of establishment of endothelial barrier    Any process that activates or increases the frequency, rate or extent of establishment of endothelial barrier.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006465    signal peptide processing    The proteolytic removal of a signal peptide from a protein during or after transport to a specific location in the cell.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005796    Golgi lumen    The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PROC_HUMAN | P040701aut 1lqv 1pcu 2pct 3f6u 3jtc
        THRB_HUMAN | P007341a2c 1a3b 1a3e 1a46 1a4w 1a5g 1a61 1abi 1abj 1ad8 1ae8 1afe 1aht 1ai8 1aix 1awf 1awh 1ay6 1b5g 1b7x 1ba8 1bb0 1bcu 1bhx 1bmm 1bmn 1bth 1c1u 1c1v 1c1w 1c4u 1c4v 1c4y 1c5l 1c5n 1c5o 1ca8 1d3d 1d3p 1d3q 1d3t 1d4p 1d6w 1d9i 1de7 1dit 1dm4 1doj 1dwb 1dwc 1dwd 1dwe 1dx5 1e0f 1eb1 1eoj 1eol 1fpc 1fph 1g30 1g32 1g37 1ghv 1ghw 1ghx 1ghy 1gj4 1gj5 1h8d 1h8i 1hag 1hah 1hai 1hao 1hap 1hbt 1hdt 1hgt 1hlt 1hut 1hxe 1hxf 1ihs 1iht 1jmo 1jou 1jwt 1k21 1k22 1kts 1ktt 1lhc 1lhd 1lhe 1lhf 1lhg 1mh0 1mu6 1mu8 1mue 1nm6 1no9 1nrn 1nro 1nrp 1nrq 1nrr 1nrs 1nt1 1nu7 1nu9 1ny2 1nzq 1o0d 1o2g 1o5g 1ook 1oyt 1p8v 1ppb 1qbv 1qhr 1qj1 1qj6 1qj7 1qur 1rd3 1riw 1sb1 1sfq 1sg8 1sgi 1shh 1sl3 1sr5 1t4u 1t4v 1ta2 1ta6 1tb6 1tbz 1thp 1thr 1ths 1tmb 1tmt 1tmu 1tom 1tq0 1tq7 1twx 1uma 1uvs 1vr1 1vzq 1w7g 1way 1wbg 1xm1 1xmn 1ype 1ypg 1ypj 1ypk 1ypl 1ypm 1z71 1z8i 1z8j 1zgi 1zgv 1zrb 2a0q 2a2x 2a45 2afq 2ank 2anm 2b5t 2bdy 2bvr 2bvs 2bvx 2bxt 2bxu 2c8w 2c8x 2c8y 2c8z 2c90 2c93 2cf8 2cf9 2cn0 2feq 2fes 2gde 2gp9 2h9t 2hgt 2hnt 2hpp 2hpq 2hwl 2jh0 2jh5 2jh6 2od3 2pgb 2pgq 2pks 2pw8 2r2m 2thf 2uuf 2uuj 2uuk 2v3h 2v3o 2zc9 2zda 2zdv 2zf0 2zff 2zfp 2zfq 2zfr 2zg0 2zgb 2zgx 2zhe 2zhf 2zhq 2zhw 2zi2 2ziq 2znk 2zo3 3b23 3b9f 3bef 3bei 3bf6 3biu 3biv 3bv9 3c1k 3c27 3d49 3da9 3dd2 3dhk 3dt0 3dux 3e6p 3ee0 3egk 3eq0 3f68 3gic 3gis 3hat 3hkj 3htc 3jz1 3jz2 3k65 3ldx 3lu9 3nxp 3p17 3p6z 3p70 3pmh 3po1 3qdz 3qgn 3qlp 3qto 3qtv 3qwc 3qx5 3r3g 3rlw 3rly 3rm0 3rm2 3rml 3rmm 3rmn 3rmo 3s7h 3s7k 3sha 3shc 3si3 3si4 3sqe 3sqh 3sv2 3t5f 3tu7 3u69 3u8o 3u8r 3u8t 3u98 3u9a 3utu 3uwj 3vxe 3vxf 4ax9 4ayv 4ayy 4az2 4bah 4bak 4bam 4ban 4bao 4baq 4boh 4ch2 4ch8 4dih 4dii 4dy7 4e05 4e06 4e7r 4h6s 4h6t 4hfp 4htc 4hzh 4i7y 4loy 4lxb 4lz1 4lz4 4mlf 4n3l 4nze 4nzq 4o03 4rkj 4rko 4rn6 4thn 4ud9 4udw 4ue7 4ueh 4ufd 4ufe 4uff 4ufg 4yes 5a2m 5af9 5afy 5afz 5ahg 5cmx 5do4 5e8e 5edk 5edm 5ew1 5ew2 5gds 5gim 5jdu 5jfd 5jzy 5l6n 5luw 5luy 5nhu 5to3 7kme 8kme

(-) Related Entries Specified in the PDB File

1shh SLOW FORM OF THROMBIN BOUND WITH PPACK