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(-) Description

Title :  HYPERSTABLE IN-FRAME INSERTION VARIANT OF ANTITHROMBIN
 
Authors :  I. Martinez-Martinez, D. J. D. Johnson, M. Yamasaki, J. Corral, J. A. Hu
Date :  23 Mar 12  (Deposition) - 18 Jul 12  (Release) - 19 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  I,L
Biol. Unit 1:  I  (1x)
Biol. Unit 2:  L  (1x)
Keywords :  Serpin, Hydrolase Inhibitor, Blood Clotting (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. Martinez-Martinez, D. J. Johnson, M. Yamasaki, J. Navarro-Fernandez, A. Ordonez, V. Vicente, J. A. Huntington, J. Corral
Type Ii Antithrombin Deficiency Caused By A Large In-Frame Insertion: Structural, Functional And Pathological Relevance.
J. Thromb. Haemost. V. 10 1859 2012
PubMed-ID: 22758787  |  Reference-DOI: 10.1111/J.1538-7836.2012.04839.X

(-) Compounds

Molecule 1 - ANTITHROMBIN-III
    ChainsI
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK-EBNA
    Expression System Taxid9606
    FragmentSEE REMARK 999
    GeneSERPINC1, AT3, PRO0309
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymATIII, SERPIN C1
 
Molecule 2 - ANTITHROMBIN-III
    ChainsL
    FragmentUNP RESIDUES 33-464
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLATENT ALPHA ANTITHROMBIN, ATIII, SERPIN C1
    TissuePLASMA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit IL
Biological Unit 1 (1x)I 
Biological Unit 2 (1x) L

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN I:96BINDING SITE FOR RESIDUE NAG I 801
2AC2SOFTWAREASN I:18 , MET I:20 , ASN I:155 , ALA I:364 , NAG I:803BINDING SITE FOR RESIDUE NAG I 802
3AC3SOFTWAREASN I:18 , PRO I:19 , NAG I:802BINDING SITE FOR RESIDUE NAG I 803
4AC4SOFTWAREASN I:192BINDING SITE FOR RESIDUE NAG I 804
5AC5SOFTWAREASN L:18 , PRO L:19 , MET L:20 , ASN L:155 , ALA L:356 , NAG L:502BINDING SITE FOR RESIDUE NAG L 501
6AC6SOFTWAREASN L:18 , PRO L:19 , NAG L:501BINDING SITE FOR RESIDUE NAG L 502

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1I:8 -I:128
2I:21 -I:95
3I:255 -I:438
4L:8 -L:128
5L:21 -L:95
6L:247 -L:430

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4EB1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EB1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EB1)

(-) Exons   (0, 0)

(no "Exon" information available for 4EB1)

(-) 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 I from PDB  Type:PROTEIN  Length:411
                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4eb1i_ I: Antithrombin                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................hhhhhhhhhhhhhhhhhhhhhhhh......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh......eeeeeeeeeeee.....hhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhh.....eeeeeeeeeee....eeeeeeeeeeeeee.....hhhhheeeeee.....eeeeeeeeeeeeeeeee.hhh.eeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhhh.eeeeeeeeee..eeeeeeehhhhhhhh..hhhhh.....hhhhh..eeeeeeeeeeeee....ee.......eee.........eeee....eeeeeee....eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eb1 I   5 VDICTAKPRDIPMNPMCIYRSPENRRVWELSKANSRFATTFYQHLADSKNDNDNIFLSPLSISTAFAMTKLGACNDTLQQLMEVFKFDTISEKTSDQIHFFFAKLNCRLYRKANKASKLVSANRLFGDKSLTFNETYQDISELVYGAKLQPLDFKENAEQSRAAINKWVSNKTEDVIPSEAINVLVLVNTRTSTVLVLVNTIYFKGLWKSKFSPENTRKELFYKADGESCSASMMYQEGKFRYRRVAEGTQVLELPFKGDDITMVLILPKPEKSLAKVEKELTPEVLQEWLDELEEMMLVVHMPRFRIEDGFSLKEQLQDMGLVDLFSPEKSKLPGIVADLYVSDAFHKAFLEVNEEGSEAAASTAVVIAGRSLNPNRVTFKANRPFLVFIREVPLNTIIFMGRVANPCVK 440
                                    14        24  ||    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191   ||  205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       369       379       389       399       409       419       429       439 
                                                 27|                                                                                                                                                   195|                                                                                                                                                                 364|                                                                       
                                                  45                                                                                                                                                    200                                                                                                                                                                  369                                                                       

Chain L from PDB  Type:PROTEIN  Length:392
                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4eb1l_ L: Antithrombin                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhhhhhhhhhhh......eeehhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...eeeeeeeeeee...eehhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh..................eeeeeeeeeeee.....hhhhheeeeee.....eeeeeeeeeeeeeeeee.hhh.eeeeee.....eeeeeee.....hhhhhhh..hhhhhhhhhhhheeeeeeeeeeeeeeeeeeehhhhhhhh..hhhhh.........eee.....eeeeeeeeeeee...eeeeeeeeeeee...........eeeeeee....eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eb1 L   7 ICTAKPIPMNPMCIYTNRRVWELSKANSRFATTFYQHLADSKNDNDNIFLSPLSISTAFAMTKLGACNDTLQQLMEVFKFDTISEKTSDQIHFFFAKLNCRLYRKSSKLVSANRLFGDKSLTFNETYQDISELVYGAKLQPLDFKENAEQSRAAINKWVSNKTEGRITDVIPSEAINELTVLVLVNTIYFKGLWKSKFSPENTRKELFYKADGESCSASMMYQEGKFRYRRVAEGTQVLELPFKGDDITMVLILPKPEKSLAKVEKELTPEVLQEWLDELEEMMLVVHMPRFRIEDGFSLKEQLQDMGLVDLFSPEKSKLPGIVAERDDLYVSDAFHKAFLEVNEEGSEAAASTAVVIAGRSLFKANRPFLVFIREVPLNTIIFMGRVANPC 430
                                 || 18    ||  48        58        68        78        88        98       108       118       128   ||  141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351     ||362       372       382       392  ||   408       418       428  
                                12|      23|                                                                                     132|                                                                                                                                                                                                                          357|                                 395|                            
                                 15       44                                                                                      136                                                                                                                                                                                                                           359                                  402                            

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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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EB1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EB1)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        ANT3_HUMAN | P010081ant 1ath 1azx 1br8 1dzg 1dzh 1e03 1e04 1e05 1jvq 1lk6 1nq9 1oyh 1r1l 1sr5 1t1f 1tb6 2ant 2b4x 2b5t 2beh 2gd4 2hij 2znh 3evj 3kcg

(-) Related Entries Specified in the PDB File

1e04 LATENT ANTITHROMBIN USED FOR MOLECULAR REPLACEMENT