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(-) Description

Title :  FACTOR XIA (PICHIA PASTORIS; C500S [C122S]) IN COMPLEX WITH THE INHIBITOR (2E)-N-{(1S)-1-[4-(3-AMINO-1H-INDAZOL-6-YL)-1H-IMIDAZOL-2-YL]-2-PHENYLETHYL}-3-[5-CHLORO-2-(1H-TETRAZOL-1-YL)PHENYL]PROP-2-ENAMIDE
 
Authors :  S. Sheriff
Date :  08 Dec 14  (Deposition) - 18 Feb 15  (Release) - 01 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Serine Protease, Blood Coagulation Factor, Protein Inhibitor Complex, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Pinto, J. M. Smallheer, J. R. Corte, E. J. Austin, C. Wang, T. Fang, L. M. Smith, K. A. Rossi, A. R. Rendina, J. M. Bozarth, G. Zhang, A. Wei, V. Ramamurthy, S. Sheriff, J. E. Myers, P. E. Morin, J. M. Luettgen, D. A. Seiffert, M. L. Quan, R. R. Wexler
Structure-Based Design Of Inhibitors Of Coagulation Factor Xia With Novel P1 Moieties.
Bioorg. Med. Chem. Lett. V. 25 1635 2015
PubMed-ID: 25728130  |  Reference-DOI: 10.1016/J.BMCL.2015.01.028
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COAGULATION FACTOR XI, LIGHT CHAIN
    Chains: A, B
    EC Number: 3.4.21.27
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Common: PICHIA PASTORIS
    Expression System Plasmid: PPICZALPHAA
    Expression System Strain: SMD1168H
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Gene: F11
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: FXI,PLASMA THROMBOPLASTIN ANTECEDENT,PTA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
13YU2Ligand/Ion(2E)-N-{(1S)-1-[4-(3-AMINO-1H-INDAZOL-6-YL)-1H-IMIDAZOL-2-YL]-2-PHENYLETHYL}-3-[5-CHLORO-2-(1H-TETRAZOL-1-YL)PHENYL]PROP-2-ENAMIDE
2CIT1Ligand/IonCITRIC ACID
3GOL6Ligand/IonGLYCEROL
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
13YU1Ligand/Ion(2E)-N-{(1S)-1-[4-(3-AMINO-1H-INDAZOL-6-YL)-1H-IMIDAZOL-2-YL]-2-PHENYLETHYL}-3-[5-CHLORO-2-(1H-TETRAZOL-1-YL)PHENYL]PROP-2-ENAMIDE
2CIT1Ligand/IonCITRIC ACID
3GOL1Ligand/IonGLYCEROL
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
13YU1Ligand/Ion(2E)-N-{(1S)-1-[4-(3-AMINO-1H-INDAZOL-6-YL)-1H-IMIDAZOL-2-YL]-2-PHENYLETHYL}-3-[5-CHLORO-2-(1H-TETRAZOL-1-YL)PHENYL]PROP-2-ENAMIDE
2CIT-1Ligand/IonCITRIC ACID
3GOL5Ligand/IonGLYCEROL
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:36A , PRO A:36B , ARG A:39 , HIS A:40 , LEU A:41 , HIS A:57 , TYR A:143 , ILE A:151 , ASP A:189 , ALA A:190 , CYS A:191 , LYS A:192 , GLY A:193 , ASP A:194 , SER A:195 , TRP A:215 , GLY A:216 , GLY A:218 , CYS A:219 , GLY A:226 , VAL A:227 , HOH A:402 , HOH A:432 , HOH A:437 , HOH A:458binding site for residue 3YU A 302
02AC2SOFTWAREILE A:132 , TYR A:133 , THR A:134 , LYS A:169 , HIS A:203 , HOH A:422 , HOH A:441 , HOH A:480binding site for residue CIT A 303
03AC3SOFTWAREARG A:24 , GLY A:25 , GLU A:26 , TRP A:27 , PRO A:28 , GLN A:30 , ILE A:70 , LEU A:155 , HOH A:478 , HOH A:503binding site for residue GOL A 304
04AC4SOFTWARESER B:36A , PRO B:36B , ARG B:39 , HIS B:40 , LEU B:41 , HIS B:57 , TYR B:143 , ILE B:151 , ASP B:189 , ALA B:190 , CYS B:191 , LYS B:192 , GLY B:193 , ASP B:194 , SER B:195 , TRP B:215 , GLY B:216 , GLY B:218 , CYS B:219 , GLY B:226 , VAL B:227 , HOH B:408 , HOH B:423 , HOH B:424 , HOH B:434binding site for residue 3YU B 302
05AC5SOFTWAREARG B:24 , GLY B:25 , GLU B:26 , TRP B:27 , PRO B:28 , GLN B:30 , ILE B:70 , LEU B:155 , HOH B:445 , HOH B:482binding site for residue GOL B 303
06AC6SOFTWAREGLU B:26 , TRP B:137 , LYS B:157 , TRP B:207 , HOH B:417 , HOH B:527binding site for residue GOL B 304
07AC7SOFTWARETRP B:29 , PRO B:120 , ILE B:121 , SER B:122 , VAL B:206 , TRP B:207binding site for residue GOL B 305
08AC8SOFTWAREARG A:172 , ILE B:47 , GLY B:48 , TRP B:51 , LEU B:123 , THR B:242binding site for residue GOL B 306
09AC9SOFTWAREPRO B:124 , ASP B:128 , ARG B:129 , VAL B:131 , TYR B:133 , ILE B:181 , ASN B:230 , VAL B:232 , HOH B:441binding site for residue GOL B 307
10AD1SOFTWAREASN A:72 , ASN A:153 , HOH A:418 , GLN B:50 , GLN B:86 , GLU B:109binding site for Mono-Saccharide NAG A 301 bound to ASN A 72
11AD2SOFTWAREGLN A:50 , GLN A:86 , GLU A:109 , ASN B:72 , ASN B:153 , HOH B:415binding site for Mono-Saccharide NAG B 301 bound to ASN B 72

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:42 -A:58
2A:136 -A:201
3A:168 -A:182
4A:191 -A:219
5B:42 -B:58
6B:136 -B:201
7B:168 -B:182
8B:191 -B:219

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ser A:36A-Pro A:36B
2Ser B:36A-Pro B:36B
3Val B:131 -Ile B:132

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X6P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X6P)

(-) Exons   (0, 0)

(no "Exon" information available for 4X6P)

(-) 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:236
                                                                                                                                                                                                                                                                             
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee.....eeeeeeeeee..eeeehhhhhh...hhh.eeee....hhhhh........eeeeee.....hhhhh...eeeee................hhhhh......eeeee..............eeee..eehhhhhhhhh........eeee................eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4x6p A   16 IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYTDSQRPISLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQ  243
                                    25        35 ||     43        53     || 61    ||  69        79        89        99       109       119       129       139   ||  150       160       169       179     ||187       197       207       217       227       237      
                                               36A|                    58A|     65A|                                                                           143|                    168A             184A|                                                           
                                                36B                     58B      65B                                                                            145                                      184B                                                           


Chain B from PDB  Type:PROTEIN  Length:236
                                                                                                                                                                                                                                                                             
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee.....eeeeeeeeee..eeeehhhhhh...hhh.eeee....hhhhh........eeeeee.....hhhhh...eeeee................hhhhh......eeeee..............eeee..eehhhhhhhhh........eeee................eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4x6p B   16 IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYTDSQRPISLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQ  243
                                    25        35 ||     43        53     || 61    ||  69        79        89        99       109       119       129       139   ||  150       160       169       179     ||187       197       207       217       227       237      
                                               36A|                    58A|     65A|                                                                           143|                    168A             184A|                                                           
                                                36B                     58B      65B                                                                            145                                      184B
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  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 4X6P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X6P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X6P)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        FA11_HUMAN | P03951: 1xx9 1xxd 1xxf 1zhm 1zhp 1zhr 1zjd 1zlr 1zmj 1zml 1zmn 1zom 1zpb 1zpc 1zpz 1zrk 1zsj 1zsk 1zsl 1ztj 1ztk 1ztl 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 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

4x6m 4x6n 4x6o