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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  HUMAN FACTOR XA COMPLEXED WITH 2-[3-(15N-AMINO-15N-IMINO-13C-METHYL)PHENOXY]-6-[3-(15N-AMINO-13C-METHYL)PHENOXY]-3, 5-DIFLUORO-4-METHYLPYRIDINE (ZK-806299), BINDING MODEL FROM DOUBLE REDOR NMR AND MD SIMULATIONS.
 
Authors :  L. M. Mcdowell, M. A. Mccarrick, D. R. Studelska, R. D. O'Connor, D. R. Light, W. J. Guilford, J. L. Dallas, B. Poliks, J. Schaefer
Date :  19 Sep 02  (Deposition) - 25 Feb 03  (Release) - 25 Feb 03  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,_#  (2x)
#:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Protein Inhibitor Complex, Blood Coagulation Factor, Serine Protease Class, Redor, Nmr, Molecular Dynamics (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. M. Mcdowell, M. A. Mccarrick, D. R. Studelska, R. D. O'Connor, D. R. Light, W. J. Guilford, D. Arnaiz, M. Adler, J. L. Dallas, B. Poliks, J. Schaefer
Human Factor Xa Bound Amidine Inhibitor Conformation By Double Rotational-Echo Double Resonance Nuclear Magnetic Resonance And Molecular Dynamics Simulations.
J. Med. Chem. V. 46 359 2003
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COAGULATION FACTOR XA
    ChainsA
    EC Number3.4.21.6
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Other DetailsPURCHASED FROM ENZYME RESEARCH LABS (SOUTH BEND, IN)
    SecretionBLOOD
    SynonymSTUART FACTOR

 Structural Features

(-) Chains, Units

  
Theoretical Model (2x)
#:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

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

Theoretical Model (1, 1)
No.NameCountTypeFull Name
1ZK91Ligand/Ion[3-AMINOMETHYLPHENYL-OXY-]-[BENZAMIDIN-3-YLOXY]-3,5-DIFLUORO-4-METHYL-PYRIDINE

(-) Sites  (0, 0)

(no "Site" information available for 1MSX)

(-) SS Bonds  (4, 4)

Theoretical Model
No.Residues
1A:22 -A:27
2A:42 -A:58
3A:168 -A:182
4A:191 -A:220

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1MSX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (19, 19)

Theoretical Model (19, 19)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_075213G262DFA10_HUMANUnclassified (FA10D)  ---AG43D
02UniProtVAR_065437G289RFA10_HUMANDisease (FA10D)121964946AG69R
03UniProtVAR_065438E304KFA10_HUMANDisease (FA10D)747292771AE84K
04UniProtVAR_065439D322NFA10_HUMANDisease (FA10D)121964942AD102N
05UniProtVAR_065440R327WFA10_HUMANDisease (FA10D)770119164AR107W
06UniProtVAR_065441V338MFA10_HUMANDisease (FA10D)121964947AV118M
07UniProtVAR_065442E350KFA10_HUMANDisease (FA10D)372309538AE129K
08UniProtVAR_065443T358MFA10_HUMANDisease (FA10D)768222784AT135M
09UniProtVAR_065444G363SFA10_HUMANDisease (FA10D)  ---AG140S
10UniProtVAR_065445R366CFA10_HUMANDisease (FA10D)104894392AR143C
11UniProtVAR_065446S374PFA10_HUMANDisease (FA10D)121964941AS152P
12UniProtVAR_072751V382AFA10_HUMANDisease (FA10D)  ---AV160A
13UniProtVAR_065447P383SFA10_HUMANDisease (FA10D)121964940AP161S
14UniProtVAR_065448C390FFA10_HUMANDisease (FA10D)199778916AC168F
15UniProtVAR_065449C404RFA10_HUMANDisease (FA10D)  ---AC182R
16UniProtVAR_065450G406SFA10_HUMANDisease (FA10D)376163818AG184S
17UniProtVAR_065451G420RFA10_HUMANDisease (FA10D)750759634AG196R
18UniProtVAR_072752G421DFA10_HUMANDisease (FA10D)758726161AG197D
19UniProtVAR_065452K448NFA10_HUMANDisease (FA10D)  ---AK224N

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

(-) PROSITE Motifs  (3, 3)

Theoretical Model (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.FA10_HUMAN235-467  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.FA10_HUMAN272-277  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.FA10_HUMAN413-424  1A:189-200

(-) Exons   (3, 3)

Theoretical Model (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003755591bENSE00001885902chr13:113777132-113777239108FA10_HUMAN1-24240--
1.2ENST000003755592ENSE00001757906chr13:113783766-113783926161FA10_HUMAN24-77540--
1.4ENST000003755594ENSE00001666002chr13:113792771-11379279525FA10_HUMAN78-8690--
1.5ENST000003755595ENSE00001614193chr13:113793671-113793784114FA10_HUMAN86-124390--
1.6cENST000003755596cENSE00000862532chr13:113795233-113795364132FA10_HUMAN124-168450--
1.7aENST000003755597aENSE00001710199chr13:113798165-113798409245FA10_HUMAN168-249821A:16-3015
1.8eENST000003755598eENSE00000862534chr13:113801693-113801810118FA10_HUMAN250-289401A:31-6940
1.9cENST000003755599cENSE00001616173chr13:113803230-113803843614FA10_HUMAN289-4882001A:69-245 (gaps)183

(-) Sequences/Alignments

Theoretical Model
   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:235
 aligned with FA10_HUMAN | P00742 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:235
                                   244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464     
          FA10_HUMAN    235 IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKTR  469
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee....eeeeeee....eeeehhhhhhh...eeeee............eee.eeeeee.............eeeee................hhhhhhhhh....eeeeee..............eeeeeeeehhhhhhhhh.......eeee................eeeeee..eeeeeeeeeeeeeeee..eeeeeee...hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------D--------------------------R--------------K-----------------N----W----------M-----------K-------M----S--C-------P-------AS------F-------------R-S-------------RD--------------------------N--------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 235-467                                                                                                                                                                                              -- PROSITE (1)
                PROSITE (2) -------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.7a      Exon 1.8e  PDB: A:31-69 UniProt: 250-289------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.9c  PDB: A:69-245 (gaps) UniProt: 289-488 [INCOMPLETE]                                                                                                                         Transcript 1 (2)
                1msx A   16 IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKTR  245
                                    25        35        45        55      | 64        74        84        94       104       114       124|     131B       141     ||152       162       172       182   ||  190       200       210       221  |    230       240     
                                                                        61A                                                            124A    131A|             147|                                 185A|                              218|   |                      
                                                                                                                                                131B              149                                  185B                               220   |                      
                                                                                                                                                                                                                                             223A                      

   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 1MSX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1MSX)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Theoretical Model(hide GO term definitions)
Chain A   (FA10_HUMAN | P00742)
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:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
    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:0007598    blood coagulation, extrinsic pathway    A protein activation cascade that contributes to blood coagulation and consists of the self-limited process linking exposure and activation of tissue factor to the activation of clotting factor X.
    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:0017187    peptidyl-glutamic acid carboxylation    The gamma-carboxylation of peptidyl-glutamic acid; catalyzed by the vitamin K dependent gamma-glutamyl carboxylase.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0051897    positive regulation of protein kinase B signaling    Any process that activates or increases the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    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: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: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:0031233    intrinsic component of external side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that penetrate the external side of the plasma membrane only, either directly or via some covalently attached hydrophobic anchor.
    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
        FA10_HUMAN | P007421c5m 1ezq 1f0r 1f0s 1fax 1fjs 1fxy 1g2l 1g2m 1hcg 1ioe 1iqe 1iqf 1iqg 1iqh 1iqi 1iqj 1iqk 1iql 1iqm 1iqn 1ksn 1lpg 1lpk 1lpz 1lqd 1mq5 1mq6 1nfu 1nfw 1nfx 1nfy 1nl8 1p0s 1v3x 1wu1 1xka 1xkb 1z6e 2bmg 2boh 2bok 2bq6 2bq7 2bqw 2cji 2d1j 2ei6 2ei7 2ei8 2fzz 2g00 2gd4 2h9e 2j2u 2j34 2j38 2j4i 2j94 2j95 2jkh 2p16 2p3f 2p3t 2p3u 2p93 2p94 2p95 2phb 2pr3 2q1j 2ra0 2uwl 2uwo 2uwp 2vh0 2vh6 2vvc 2vvu 2vvv 2vwl 2vwm 2vwn 2vwo 2w26 2w3i 2w3k 2wyg 2wyj 2xbv 2xbw 2xbx 2xby 2xc0 2xc4 2xc5 2y5f 2y5g 2y5h 2y7x 2y7z 2y80 2y81 2y82 3cen 3cs7 3ens 3ffg 3hpt 3iit 3k9x 3kl6 3kqb 3kqc 3kqd 3kqe 3liw 3m36 3m37 3q3k 3sw2 3tk5 3tk6 4a7i 4bti 4btt 4btu 4y6d 4y71 4y76 4y79 4y7a 4y7b 4zh8 4zha 5jqy 5jtc 5jz8 5jzu 5k0h

(-) Related Entries Specified in the PDB File

1cu7 TRYPSIN COMPLEXED WITH THE SAME INHIBITOR, THE MD FOR THE PRESENT MODELS USED TWO CONFORMATIONS OF INHIBITOR OF 1CU7 AS STARTING CONFORMATIONS.
1cu8 TRYPSIN COMPLEXED WITH ZK-805623
1fax THE SAME PROTEIN COMPLEXED WITH DX-9065A
1fjs THE SAME PROTEIN COMPLEXED WITH ZK-807834
1xka THE SAME PROTEIN COMPLEXED WITH FX-2212A, THE MD FOR THE PRESENT MODELS USED ENZYME COORDINATES OF 1XKA AS STARTING COORDINATES.