Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  SHARK IGNAR VARIABLE DOMAIN
 
Authors :  A Olland, O. V. Kovalenko, D. King, K. Svenson
Date :  08 Oct 12  (Deposition) - 08 May 13  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.34
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ig-Fold, Human Albumin, V-Nar, 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 - SHARK V-NAR
    Chains: A
    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
 
Molecule 2 - SERUM ALBUMIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:150 , ARG B:257 , ALA B:291BINDING SITE FOR RESIDUE EDO B 601
2AC2SOFTWAREGLY B:248 , ASP B:249 , LEU B:250 , LEU B:251 , GLU B:252BINDING SITE FOR RESIDUE ACE B 602

(-) SS Bonds  (16, 16)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:83
2B:53 -B:62
3B:75 -B:91
4B:90 -B:101
5B:124 -B:169
6B:168 -B:177
7B:200 -B:246
8B:245 -B:253
9B:265 -B:279
10B:278 -B:289
11B:316 -B:361
12B:360 -B:369
13B:392 -B:438
14B:437 -B:448
15B:461 -B:477
16B:476 -B:487

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:6 -Pro A:7
2Glu B:95 -Pro B:96

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HGM)

(-) Sequences/Alignments

Asymmetric/Biological 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:103
                                                                                                                                       
               SCOP domains d4hgma_ A: automated matches                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeee.....eeeeeeee.....eeeeeeeee.......ee......eeeeee....eeeeee...hhhhh.eeeeeeee....eee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 4hgm A   1 TRVDQSPSSLSASVGDRVTITCVLTDTSYPLYSTYWYQQKPGSSNKEQISISGRYSESVNKGTKSFTLTISSLQPEDFATYYCRAMGTNIWTGDGAGTKVEIK 103
                                    10        20        30        40        50        60        70        80        90       100   


Chain B from PDB  Type:PROTEIN  Length:479
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4hgmb1 B:4-196 Serum albumin                                                                                                                                                             d4hgmb2 B:197-388 Serum albumin                                                                                                                                                                 d4hgmb3 B:389-492 Serum albumin                                                                     - SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh......hhhhh..hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...........hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hgm B   4 KSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVAEMADCCAKQEPERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFEQLGEYQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVVLNQLCVLHEKTPVSDRVTKCCSLVNRRPCFSALEx 602
                                    13        23        33        43        53        63        73    ||  90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400||     412       422       432       442       452       462       472    || 484       ||
                                                                                                     78|                                                                                                                                                                                                                                                                                                                        401|                                                                      477|         492|
                                                                                                      86                                                                                                                                                                                                                                                                                                                         404                                                                       480          602-ACE
   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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ACE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu B:95 - Pro B:96   [ RasMol ]  
    Ser A:6 - Pro A:7   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4hgm
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ALBU_HUMAN | P02768
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  ALBU_HUMAN | P02768
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 4hgk 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

4hgk