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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF COAGULATION FACTOR XI IN COMPLEX WITH N-[4-GUANIDINO-1-(THIAZOLE-2-CARBONYL)-BUTYL]-2-{6-OXO-5-[(QUINOLIN-8-YLMETHYL)-AMINO]-2-M-TOLYL-6H-PYRIMIDIN-1-YL}-ACETAMIDE
 
Authors :  P. Nagafuji, L. Jin, M. Rynkiewicz, J. Quinn, F. Bibbins, H. Meyers, R. Babine, J. E. Strickler, S. S. Abdel-Meguid
Date :  27 May 05  (Deposition) - 09 May 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Fxia, Inhibitors, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Nagafuji, L. Jin, M. Rynkiewicz, J. Quinn, F. Bibbins, H. Meyers, R. Babine, J. E. Strickler, S. S. Abdel-Meguid
Pyrimidinone Inhibitors Of A Thrombolytic Protease
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COAGULATION FACTOR XI
    ChainsA
    EC Number3.4.21.27
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System StrainX-33
    Expression System Taxid4922
    FragmentCATALYTIC DOMAIN
    GeneF11
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPLASMA THROMBOPLASTIN ANTECEDENT, PTA, FXI

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
17371Ligand/IonN-[4-GUANIDINO-1-(THIAZOLE-2-CARBONYL)-BUTYL]-2-{6-OXO-5-[(QUINOLIN-8-YLMETHYL)-AMINO]-2-M-TOLYL-6H-PYRIMIDIN-1-YL}-ACETAMIDE
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:20 , ALA A:21 , GLN A:48 , GLN A:86 , LYS A:107BINDING SITE FOR RESIDUE SO4 A 246
2AC2SOFTWAREASN A:113 , LYS A:149 , LYS A:192BINDING SITE FOR RESIDUE SO4 A 247
3AC3SOFTWAREHIS A:57 , ALA A:115 , ASP A:189 , ALA A:190 , CYS A:191 , LYS A:192 , GLY A:193 , ASP A:194 , SER A:195 , SER A:214 , TRP A:215 , GLY A:216 , GLY A:218 , CYS A:219 , GLY A:226 , HOH A:254 , HOH A:300BINDING SITE FOR RESIDUE 737 A 248

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:40 -A:58
2A:136 -A:201
3A:168 -A:182
4A:191 -A:219

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:37 -Pro A:37A

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (25, 25)

Asymmetric/Biological Unit (25, 25)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_011778W399RFA11_HUMANPolymorphism1800439AW27R
02UniProtVAR_067945W401RFA11_HUMANDisease (FA11D)281875262AW29R
03UniProtVAR_067946V403MFA11_HUMANDisease (FA11D)281875266AV31M
04UniProtVAR_012092T404NFA11_HUMANDisease (FA11D)121965067AT32N
05UniProtVAR_054901G418VFA11_HUMANDisease (FA11D)121965071AG42V
06UniProtVAR_012093A430VFA11_HUMANDisease (FA11D)121965068AA56V
07UniProtVAR_067947I454KFA11_HUMANDisease (FA11D)281875241AI77K
08UniProtVAR_012094F460VFA11_HUMANDisease (FA11D)121965065AF82V
09UniProtVAR_067948I481SFA11_HUMANDisease (FA11D)281875242AI103S
10UniProtVAR_012095T493IFA11_HUMANDisease (FA11D)  ---AA115I
11UniProtVAR_067949S503PFA11_HUMANDisease (FA11D)140068026AS126P
12UniProtVAR_067950D506GFA11_HUMANDisease (FA11D)281875258AD129G
13UniProtVAR_054902Y511HFA11_HUMANDisease (FA11D)281875278AY133H
14UniProtVAR_067951C514FFA11_HUMANDisease (FA11D)281875249AC136F
15UniProtVAR_067952D526EFA11_HUMANDisease (FA11D)281875263AD148E
16UniProtVAR_054903P538LFA11_HUMANDisease (FA11D)139695003AP161L
17UniProtVAR_076518E543KFA11_HUMANDisease (FA11D)142952627AE166K
18UniProtVAR_076519H552RFA11_HUMANDisease (FA11D)369935706AH174R
19UniProtVAR_054904E565KFA11_HUMANDisease (FA11D)281875275AE186K
20UniProtVAR_067953S575LFA11_HUMANDisease (FA11D)281875250AS195L
21UniProtVAR_054905W587SFA11_HUMANDisease (FA11D)121965072AW203S
22UniProtVAR_012096S594RFA11_HUMANDisease (FA11D)28934609AS214R
23UniProtVAR_067954E597KFA11_HUMANDisease (FA11D)281875251AE217K
24UniProtVAR_067955Y608HFA11_HUMANDisease (FA11D)281875255AY228H
25UniProtVAR_054906I618SFA11_HUMANDisease (FA11D)281875276AI238S

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.FA11_HUMAN388-623  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.FA11_HUMAN427-432  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.FA11_HUMAN569-580  1A:189-198B

(-) Exons   (0, 0)

(no "Exon" information available for 1ZTL)

(-) 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:237
 aligned with FA11_HUMAN | P03951 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:237
                                   397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       
          FA11_HUMAN    388 IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYTDSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQA  624
               SCOP domains d1ztla_ A: Coagulation factor XI                                                                                                                                                                                                              SCOP domains
               CATH domains 1ztlA01     1ztlA02 A:28-121,A:234-244 Trypsin-like serine proteases                                           1ztlA01 A:16-27,A:122-233 Trypsin-like serine proteases                                                            1ztlA02     CATH domains
               Pfam domains Trypsin-1ztlA01 A:16-238                                                                                                                                                                                                               ------ Pfam domains
         Sec.struct. author ....ee........eeeeee.....eeeeeeeeee..eeee.hhhhh...hhh.eeeee...hhhhh......eeeeeeee.....hhhhh...eeeee................hhhhh.......eeee..............eeee..eehhhhhhhhh........eeee................eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------R-R-MN-------------V-----------V-----------------------K-----V--------------------S-----------I---------P--G----H--F-----------E-----------L----K--------R------------K---------L-----------S------R--K----------H---------S------ SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 388-623                                                                                                                                                                                                 - PROSITE (1)
                PROSITE (2) ---------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ztl A   16 IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQAEIAEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYADSQRPISLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQA  244
                                    25        35  ||||  41      ||53      ||60        70        80 |      89        99       109       119|      130  |    139       149|      160       170   |   179     | 188|      197 ||| ||203||     217       227       237       
                                                37A|||         48|      59A||                    81A                                   119|        132A              149|                   173A        184A 188A       198A|| |||| ||                                   
                                                 37B||          51       59B|                                                           121                           151                                                198B| |||| ||                                   
                                                  37C|                    59C                                                                                                                                              201 |||| ||                                   
                                                   37D                                                                                                                                                                      202A||| ||                                   
                                                                                                                                                                                                                             202B|| ||                                   
                                                                                                                                                                                                                              202C| ||                                   
                                                                                                                                                                                                                               202D ||                                   
                                                                                                                                                                                                                                  204|                                   
                                                                                                                                                                                                                                   209                                   

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FA11_HUMAN | P03951)
molecular function
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    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:0070009    serine-type aminopeptidase activity    Catalysis of the hydrolysis of a peptide bond not more than three residues from the N-terminus of 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: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: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:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0031639    plasminogen activation    The process in which inactive plasminogen is processed to active plasmin. This process includes cleavage at an internal Arg-Val site to form an N-terminal A-chain and C-terminal B-chain held together by a disulfide bond, and can include further proteolytic cleavage events to remove the preactivation peptide.
    GO:0051919    positive regulation of fibrinolysis    Any process that activates, maintains or increases the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots.
    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.
cellular component
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FA11_HUMAN | P039511xx9 1xxd 1xxf 1zhm 1zhp 1zhr 1zjd 1zlr 1zmj 1zml 1zmn 1zom 1zpb 1zpc 1zpz 1zrk 1zsj 1zsk 1zsl 1ztj 1ztk 2f83 2fda 2j8j 2j8l 3bg8 3sor 3sos 4cr5 4cr9 4cra 4crb 4crc 4crd 4cre 4crf 4crg 4d76 4d7f 4d7g 4na7 4na8 4ty6 4ty7 4wxi 4x6m 4x6n 4x6o 4x6p 4y8x 4y8y 4y8z 5e2o 5e2p 5eod 5eok 5exl 5exm 5exn 5i25 5q0d 5q0e 5q0f 5q0g 5q0h 5tks 5tkt 5tku

(-) Related Entries Specified in the PDB File

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