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(-) Description

Title :  SOLUTION STRUCTURE OF THE A4 DOMAIN OF BLOOD COAGULATION FACTOR XI
 
Authors :  D. Samuel, H. Cheng, P. W. Riley, A. A. Canutescu, Z. Bu, P. N. Walsh, H. Roder
Date :  25 Oct 06  (Deposition) - 02 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (14x)
Keywords :  Protease, Hydrolase, Glycoprotein, Polymorphism, Serine Protease, Heparin-Binding, Disease Mutation, Fxi / Blood Coagulation / Pan Domain /Apple Domain / Blood Coagulation, Alternative Splicing (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Samuel, H. Cheng, P. W. Riley, A. A. Canutescu, C. Nagaswami, J. W. Weisel, Z. Bu, P. N. Walsh, H. Roder
Solution Structure Of The A4 Domain Of Factor Xi Sheds Light On The Mechanism Of Zymogen Activation.
Proc. Nat. Acad. Sci. Usa V. 104 15693 2007
PubMed-ID: 17884987  |  Reference-DOI: 10.1073/PNAS.0703080104

(-) Compounds

Molecule 1 - COAGULATION FACTOR XI
    ChainsA, B
    EC Number3.4.21.27
    FragmentAPPLE 4 DOMAIN, RESIDUES 290-379
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPLASMA THROMBOPLASTIN ANTECEDENT, PTA, FXI, FACTOR XI

 Structural Features

(-) Chains, Units

  
NMR Structure (14x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2J8J)

(-) Sites  (0, 0)

(no "Site" information available for 2J8J)

(-) SS Bonds  (7, 7)

NMR Structure
No.Residues
1A:273 -A:356
2A:299 -A:328
3A:303 -A:309
4A:321 -B:321
5B:273 -B:356
6B:299 -B:328
7B:303 -B:309

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2J8J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (10, 20)

NMR Structure (10, 20)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_006622F301LFA11_HUMANDisease (FA11D)121965064A/BF283L
02UniProtVAR_011776I308FFA11_HUMANPolymorphism5972A/BI290F
03UniProtVAR_067942E315KFA11_HUMANDisease (FA11D)281875257A/BE297K
04UniProtVAR_012088L320PFA11_HUMANDisease (FA11D)281875268A/BL302P
05UniProtVAR_012089T322IFA11_HUMANDisease (FA11D)281875269A/BT304I
06UniProtVAR_012090R326CFA11_HUMANDisease (FA11D)28934608A/BR308C
07UniProtVAR_067943T331IFA11_HUMANDisease (FA11D)281875253A/BT313I
08UniProtVAR_011777C339FFA11_HUMANPolymorphism5967A/BC321F
09UniProtVAR_012091E341KFA11_HUMANDisease (FA11D)281875270A/BE323K
10UniProtVAR_067944L360PFA11_HUMANDisease (FA11D)281875254A/BL342P

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1APPLEPS00495 Apple domain.FA11_HUMAN20-103
110-193
200-283
291-374
 
  2-
-
-
A:273-356
B:273-356
2PANPS50948 PAN/Apple domain profile.FA11_HUMAN20-103
110-193
200-283
291-374
 
  2-
-
-
A:273-356
B:273-356

(-) Exons   (0, 0)

(no "Exon" information available for 2J8J)

(-) Sequences/Alignments

NMR Structure
   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:90
 aligned with FA11_HUMAN | P03951 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:90
                                   299       309       319       329       339       349       359       369       379
           FA11_HUMAN   290 FCHSSFYHDTDFLGEELDIVAAKSHEACQKLCTNAVRCQFFTYTPAQASCNEGKGKCYLKLSSNGSPTKILHGRGGISGYTLRLCKMDNE 379
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee..eeee..eeeee.....hhhhhhhhhh....eeee.............eeeee.......eeee....eeee..hhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------L------F------K----P-I---C----I-------F-K------------------P------------------- SAPs(SNPs)
                PROSITE (1) -APPLE  PDB: A:273-356 UniProt: 291-374                                              ----- PROSITE (1)
                PROSITE (2) -PAN  PDB: A:273-356 UniProt: 291-374                                                ----- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 2j8j A 272 FCHSSFYHDTDFLGEELDIVAAKSHEACQKLCTNAVRCQFFTYTPAQASCNEGKGKCYLKLSSNGSPTKILHGRGGISGYTLRLCKMDNE 361
                                   281       291       301       311       321       331       341       351       361

Chain B from PDB  Type:PROTEIN  Length:90
 aligned with FA11_HUMAN | P03951 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:90
                                   299       309       319       329       339       349       359       369       379
           FA11_HUMAN   290 FCHSSFYHDTDFLGEELDIVAAKSHEACQKLCTNAVRCQFFTYTPAQASCNEGKGKCYLKLSSNGSPTKILHGRGGISGYTLRLCKMDNE 379
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeee...eeee.....hhhhhhhhhh....eeee.............eeee........eeeeeeeeeeeee.hhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------L------F------K----P-I---C----I-------F-K------------------P------------------- SAPs(SNPs)
                PROSITE (1) -APPLE  PDB: B:273-356 UniProt: 291-374                                              ----- PROSITE (1)
                PROSITE (2) -PAN  PDB: B:273-356 UniProt: 291-374                                                ----- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 2j8j B 272 FCHSSFYHDTDFLGEELDIVAAKSHEACQKLCTNAVRCQFFTYTPAQASCNEGKGKCYLKLSSNGSPTKILHGRGGISGYTLRLCKMDNE 361
                                   281       291       301       311       321       331       341       351       361

   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 2J8J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2J8J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J8J)

(-) Gene Ontology  (19, 19)

NMR Structure(hide GO term definitions)
Chain A,B   (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 1ztl 2f83 2fda 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

1xx9 CRYSTAL STRUCTURE OF THE FXIA CATALYTIC DOMAIN IN COMPLEXWITH ECOTINM84R
1xxd CRYSTAL STRUCTURE OF THE FXIA CATALYTIC DOMAIN IN COMPLEXWITH MUTATED ECOTIN
1xxf CRYSTAL STRUCTURE OF THE FXIA CATALYTIC DOMAIN IN COMPLEXWITH ECOTIN MUTANT (ECOTINP)
1zhm CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THECOAGULATION FACTOR XIA IN COMPLEX WITH BENZAMIDINE (S434A-T475A-K437 MUTANT)
1zhp CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF COAGULATIONFACTOR XI IN COMPLEX WITH BENZAMIDINE (S434A-T475A-K505MUTANT)
1zhr CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF COAGULATIONFACTOR XI IN COMPLEX WITH BENZAMIDINE (S434A-T475A-C482S-K437A MUTANT)
1zjd CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF COAGULATIONFACTOR XI IN COMPLEX WITH KUNITZ PROTEASE INHIBITOR DOMAINOF PROTEASE NEXIN II
1zlr FACTOR XI CATALYTIC DOMAIN COMPLEXED WITH 2 -GUANIDINO-1-(4-(4,4,5,5-TETRAMETHYL-1 ,3,2-DIOXABOROLAN-2-YL)PHENYL) ETHYLNICOTINATE
1zmj CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF FACTOR XI INCOMPLEX WITH 4-(GUANIDINOMETHYL )-PHENYLBORONIC ACID
1zml CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF FACTOR XI INCOMPLEX WITH (R)-1-(4-(4-( HYDROXYMETHYL)-1,3,2-DIOXABOROLAN-2-YL) PHENETHYL)GUANIDINE
1zmn CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF COAGULATIONFACTOR XI IN COMPLEX WITH (R)-1 -(4-(4-(HYDROXYMETHYL)-1,3,2-DIOXABOROLAN- 2-YL)PHENYL)GUANIDINE
1zom CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF COAGULATIONFACTOR XI IN COMPLEX WITH A PEPTIDOMIMETIC INHIBITOR
1zpz FACTOR XI CATALYTIC DOMAIN COMPLEXED WITH N -((R)-1-(4-BROMOPHENYL)ETHYL)UREA-ASN-VAL -ARG-ALPHA-KETOTHIAZOLE
1zrk FACTOR XI COMPLEXED WITH 3-HYDROXYPROPYL 3 -(7-AMIDINONAPHTHALENE-1-CARBOXAMIDO) BENZENESULFONATE
1zsj CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF COAGULATIONFACTOR XI IN COMPLEX WITH N-(7 -CARBAMIMIDOYL-NAPHTHALEN-1-YL)-3-HYDROXY-2 -METHYL-BENZAMIDE
1zsk CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF COAGULATIONFACTOR XI IN COMPLEX WITH 6- CARBAMIMIDOYL-4-(3-HYDROXY-2-METHYL- BENZOYLAMINO)-NAPHTHALENE-2-CARBOXYLIC ACID METHYLESTER
1zsl FACTOR XI COMPLEXED WITH A PYRIMIDINONE INHIBITOR
1ztj CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF COAGULATIONFACTOR XI IN COMPLEX WITH 2-(5 -BENZYLAMINO-2-METHYLSULFANYL-6-OXO-6H- PYRIMIDIN-1-YL)-N-[4-GUANIDINO-1-(THIAZOLE -2-CARBONYL)-BUTYL]-ACETAMIDE
1ztk CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF COAGULATIONFACTOR XI IN COMPLEX WITH 2-(5 -AMINO-6-OXO-2-M-TOLYL-6H-PYRIMIDIN-1- YL)-N-[4-GUANIDINO-1-(THIAZOLE-2-CARBONYL )-BUTYL]-ACETAMIDE
1ztl CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF COAGULATIONFACTOR 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
2j8l FXI APPLE 4 DOMAIN LOOP-OUT CONFORMATION