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(-) Description

Title :  SHARK IGNAR VARIABLE DOMAIN
 
Authors :  A. O. Olland, O. V. Kovalenko, K. Svenson, D. King
Date :  08 Oct 12  (Deposition) - 08 May 13  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.04
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Ig-Fold, Human Albumin, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. V. Kovalenko, A. Olland, N. Piche-Nicholas, A. Godbole, D. King, K. Svenson, V. Calabro, M. R. Muller, C. J. Barelle, W. Somers, D. S. Gill, L. Mosyak, L. Tchistiakova
Atypical Antigen Recognition Mode Of A Shark Immunoglobulin New Antigen Receptor (Ignar) Variable Domain Characterized By Humanization And Structural Analysis.
J. Biol. Chem. V. 288 17408 2013
PubMed-ID: 23632026  |  Reference-DOI: 10.1074/JBC.M112.435289

(-) Compounds

Molecule 1 - SERUM ALBUMIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - SHARK V-NAR ANTIBODY
    Chains: C, D
    Engineered: YES
    Expression System: CHLOROCEBUS AETHIOPS
    Expression System Cell Line: COS-1
    Expression System Common: AFRICAN GREEN MONKEY
    Expression System Taxid: 9534
    Organism Common: DOGFISH SHARK
    Organism Scientific: SQUALUS ACANTHIAS
    Organism Taxid: 7797

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4HGK)

(-) Sites  (0, 0)

(no "Site" information available for 4HGK)

(-) SS Bonds  (31, 31)

Asymmetric Unit
No.Residues
1A:53 -A:62
2A:90 -A:101
3A:124 -A:169
4A:168 -A:177
5A:200 -A:246
6A:245 -A:253
7A:265 -A:279
8A:278 -A:289
9A:316 -A:361
10A:360 -A:369
11A:392 -A:438
12A:437 -A:448
13A:461 -A:477
14A:476 -A:487
15B:53 -B:62
16B:75 -B:91
17B:90 -B:101
18B:124 -B:169
19B:168 -B:177
20B:200 -B:246
21B:245 -B:253
22B:265 -B:279
23B:278 -B:289
24B:316 -B:361
25B:360 -B:369
26B:392 -B:438
27B:437 -B:448
28B:461 -B:477
29B:476 -B:487
30C:41 -C:102
31D:41 -D:102

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:95 -Pro A:96
2Glu B:95 -Pro B:96
3Thr C:25 -Pro C:26
4Thr D:25 -Pro D:26

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HGK)

(-) 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:483
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4hgka1 A:4-196 automated matches                                                                                                                                                            d4hgka2 A:197-388 automated matches                                                                                                                                                             ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhh...........hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hgk A   4 KSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLGEMADCCAKQEPERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFEQLGEYKFQNALLVRYTKKVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVVLNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEV 493
                                    13        23        33        43        53        63        73      ||87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       420       430       440       450       460       470       480       490   
                                                                                                       80|                                                                                                                                                                                                                                                                                                                                       415|                                                                          
                                                                                                        85                                                                                                                                                                                                                                                                                                                                        419                                                                          


Chain B from PDB  Type:PROTEIN  Length:481
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4hgkb1 B:4-196 automated matches                                                                                                                                                        d4hgkb2 B:197-388 automated matches                                                                                                                                                             -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh.hhhhhh...hhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...........hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hgk B   4 KSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVEMADCCAKQEPERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVVLNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALE 492
                                    13        23        33        43        53        63        73   ||   91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491 
                                                                                                    77|                                                                                                                                                                                                                                                                                                                                                                                                                      
                                                                                                     86                                                                                                                                                                                                                                                                                                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:104
                                                                                                                                        
               SCOP domains d4hgkc_ C: automated matches                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee....eeeeeeee.....eeeeeeeee.......ee......eeeeee....eeeeee...hhhhheeeeeeeee....eee...eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 4hgk C  20 TRVDQTPRTATRETGESLTINCVLTDTSYPLYSTYWYRKNPGSSNKEQISISGRYVESVNKGTKSFSLRIKDLTVADSATYICRAMGTNIWTGDGAGTVLTVNH 123
                                    29        39        49        59        69        79        89        99       109       119    


Chain D from PDB  Type:PROTEIN  Length:104
                                                                                                                                        
               SCOP domains d4hgkd_ D: automated matches                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee....eeeeeeee.....eeeeeeeee.......ee......eeeeee....eeeeee...hhhhheeeeeeeee....eee...eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 4hgk D  20 TRVDQTPRTATRETGESLTINCVLTDTSYPLYSTYWYRKNPGSSNKEQISISGRYVESVNKGTKSFSLRIKDLTVADSATYICRAMGTNIWTGDGAGTVLTVNH 123
                                    29        39        49        59        69        79        89        99       109       119
   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  (2, 6)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (45, 45)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu A:95 - Pro A:96   [ RasMol ]  
    Glu B:95 - Pro B:96   [ RasMol ]  
    Thr C:25 - Pro C:26   [ RasMol ]  
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  4hgk
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  ALBU_HUMAN | P02768
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 Related Entries

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

UniProtKB/Swiss-Prot
        ALBU_HUMAN | P02768: 1ao6 1bj5 1bke 1bm0 1e78 1e7a 1e7b 1e7c 1e7e 1e7f 1e7g 1e7h 1e7i 1gni 1gnj 1h9z 1ha2 1hk1 1hk2 1hk3 1hk4 1hk5 1n5u 1o9x 1tf0 1uor 1ysx 2bx8 2bxa 2bxb 2bxc 2bxd 2bxe 2bxf 2bxg 2bxh 2bxi 2bxk 2bxl 2bxm 2bxn 2bxo 2bxp 2bxq 2esg 2i2z 2i30 2n0x 2vdb 2vue 2vuf 2xsi 2xvq 2xvu 2xvv 2xvw 2xw0 2xw1 2ydf 3a73 3b9l 3b9m 3cx9 3jqz 3jry 3lu6 3lu7 3lu8 3sqj 3tdl 3uiv 4bke 4e99 4emx 4g03 4g04 4hgm 4iw1 4iw2 4k2c 4k71 4l8u 4l9k 4l9q 4la0 4lb2 4lb9 4n0f 4n0u 4s1y 4z69 5fuo 5id7 5ifo 5ijf 5ujb 5x52

(-) Related Entries Specified in the PDB File

4hgm