Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF EXTRACELLULAR DOMAIN OF HER2 IN COMPLEX WITH FCAB STAB19
 
Authors :  A. Humm, E. Lobner, K. Goritzer, G. Mlynek, C. Obinger, K. Djinovic-Car
Date :  19 May 16  (Deposition) - 12 Apr 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A,C  (2x)
Keywords :  Immune System, Antibody Engineering, Immunoglobulin G1, Fc Fragment, Glycosylations, Ch3 Domain, Fcab, Human Epidermal Growth Factor Receptor 2, Her2/Neu, Erbb-2, Cell Surface Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Lobner, A. S. Humm, K. Goritzer, G. Mlynek, M. G. Puchinger, C. Hasenhindl, F. Ruker, M. W. Traxlmayr, K. Djinovic-Carugo, C. Obinger
Fcab-Her2 Interaction: A Menage A Trois. Lessons From X-Ray And Solution Studies.
Structure V. 25 878 2017
PubMed-ID: 28528777  |  Reference-DOI: 10.1016/J.STR.2017.04.014

(-) Compounds

Molecule 1 - IG GAMMA-1 CHAIN C REGION
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293-6E
    Expression System Common: HUMAN
    Expression System Organ: KIDNEY
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: IGHG1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - RECEPTOR TYROSINE-PROTEIN KINASE ERBB-2
    Chains: C
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHO LEC1
    Expression System Common: RABBIT
    Expression System Taxid: 10029
    Expression System Tissue: OVARY
    Gene: ERBB2, HER2, MLN19, NEU, NGL
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: METASTATIC LYMPH NODE GENE 19 PROTEIN,MLN 19,PROTO-ONCOGENE NEU,PROTO-ONCOGENE C-ERBB-2,TYROSINE KINASE-TYPE CELL SURFACE RECEPTOR HER2,P185ERBB2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AC
Biological Unit 1 (2x): AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2GOL1Ligand/IonGLYCEROL
3MAN3Ligand/IonALPHA-D-MANNOSE
4NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (4, 24)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2GOL2Ligand/IonGLYCEROL
3MAN6Ligand/IonALPHA-D-MANNOSE
4NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:238 , SER A:239 , VAL A:240 , LYS A:334binding site for residue GOL A 506
2AC2SOFTWAREPHE A:243 , VAL A:264 , ASP A:265 , GLN A:295 , ASN A:297 , ARG A:301binding site for Poly-Saccharide residues NAG A 501 through MAN A 505 bound to ASN A 297
3AC3SOFTWAREASP C:163 , ASN C:165 , LYS C:226binding site for Mono-Saccharide NAG C 706 bound to ASN C 165
4AC4SOFTWARELEU C:231 , ALA C:232 , ASN C:237binding site for Poly-Saccharide residues NAG C 701 through MAN C 704 bound to ASN C 237
5AC5SOFTWAREHIS A:415 , ASN C:549binding site for Mono-Saccharide NAG C 705 bound to ASN C 549

(-) SS Bonds  (24, 24)

Asymmetric Unit
No.Residues
1A:261 -A:321
2A:367 -A:425
3C:4 -C:31
4C:140 -C:170
5C:173 -C:182
6C:177 -C:190
7C:198 -C:205
8C:202 -C:213
9C:214 -C:222
10C:218 -C:230
11C:233 -C:242
12C:246 -C:273
13C:277 -C:289
14C:293 -C:309
15C:312 -C:316
16C:320 -C:345
17C:453 -C:482
18C:489 -C:498
19C:493 -C:506
20C:509 -C:518
21C:522 -C:538
22C:541 -C:554
23C:545 -C:562
24C:565 -C:574

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:373 -Pro A:374

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K33)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K33)

(-) Exons   (0, 0)

(no "Exon" information available for 5K33)

(-) 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:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhh.....eeeeeeeee.......eeeeee..ee....ee..........eeeeeeee.hhhhhhh...eeeeee.......eeeee..........eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee..eee...ee.....eeeeeeeeee..hhhhhhhhh...eeeeee...hhhhheeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5k33 A  237 GPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDEYLSDSVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVPRHSETMRRWAHGNVFSCSVMHEALHNHYTQKSLSLS  444
                                   246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406      415A||||   421       431       441   
                                                                                                                                                                                                            415A||||                             
                                                                                                                                                                                                             415B|||                             
                                                                                                                                                                                                              415C||                             
                                                                                                                                                                                                               415D|                             
                                                                                                                                                                                                                415E                             


Chain C from PDB  Type:PROTEIN  Length:563
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..........hhhhhhhhhhhhhh...eee..eeee.......hhhhhhh.ee...eeee.............ee....hhhh.eeeeeee.......................ee...eeeeee..........hhhhh.........eee.......................hhhhh...........................eeeee.......eeee..eee..eee......eee......eee.....eee..eee.......ee.....ee......eeee....eeee........ee...hhhhh........hhhhhh...eee..eeehhhhhh.........hhhhhhhhh.ee...eee.........hhhhh...ee....hhhh.eeeeee.............ee...eeeee...........hhhhhh......eeee...hhhhhhh........hhhhh....hhhhh.....eee..eee...........eee....eee.................hhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5k33 C    1 TQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTATQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHDPPFCVA  576
                                    10        20        30        40        50        60        70        80        90       100 ||    115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295      |308       318       328       338       348       358    || 371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561     ||573   
                                                                                                                               102|                                                                                                                                                                                               302|                                                      363|                                                                                                                                                                                                     567|      
                                                                                                                                108                                                                                                                                                                                                306                                                       367                                                                                                                                                                                                      570
   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 5K33)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K33)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K33)

(-) Gene Ontology  (92, 93)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    BMA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Tyr A:373 - Pro A:374   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  5k33
    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
  ERBB2_HUMAN | P04626
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  IGHG1_HUMAN | P01857
    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)
  2.7.10.1
    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
  ERBB2_HUMAN | P04626
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  IGHG1_HUMAN | P01857
    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
        ERBB2_HUMAN | P04626: 1mfg 1mfl 1mw4 1n8z 1ovc 1qr1 1s78 2a91 2jwa 2ks1 2l4k 2n2a 3be1 3h3b 3mzw 3n85 3pp0 3rcd 3wlw 3wsq 4gfu 4hrl 4hrm 4hrn 4nnd 5kwg
        IGHG1_HUMAN | P01857: 1aj7 1aqk 1axs 1bey 1d5b 1d5i 1d6v 1dfb 1dn2 1e4k 1fc1 1fc2 1fcc 1gaf 1h3t 1h3u 1h3v 1h3w 1h3x 1h3y 1hkl 1hzh 1i7z 1l6x 1n7m 1op3 1oqo 1oqx 1pg7 1t83 1t89 1vge 2dts 2gj7 2i5y 2iwg 2j6e 2jb5 2jb6 2o5x 2o5y 2o5z 2osl 2qad 2ql1 2qqk 2qql 2qqn 2qr0 2r56 2rcj 2rcs 2vxq 2wah 3agv 3ave 3ay4 3b2u 3b2v 3bdy 3be1 3bky 3bn9 3bqu 3c08 3c09 3c2s 3cfj 3cfk 3csy 3d0l 3d0v 3d6g 3d85 3dj9 3dnk 3do3 3dro 3drq 3dvg 3dvn 3eyf 3eyo 3eyq 3fjt 3mcl 3o11 3ry6 3s7g 3sgj 3sgk 3tv3 3twc 3tyg 3u0w 3u7w 3u7y 3v7m 3v8c 3v95 3wjj 3wjl 3wkn 3wn5 4acp 4b7i 4bm7 4bsv 4bsw 4byh 4cdh 4d9q 4d9r 4dag 4dz8 4eow 4hix 4j12 4ku1 4lld 4llm 4llq 4n0u 4nqs 4nqt 4nqu 4nwt 4nwu 4o4y 4o51 4q6y 4q74 4q7d 4w4n 4w4o 4wi2 4wi3 4wi4 4wi5 4wi6 4wi7 4wi8 4wi9 4x4m 4x98 4x99 4xmp 4xny 4xnz 4xxd 4zne 5bw7 5c7k 5d4q 5d6d 5di8 5dj0 5dj2 5dj6 5dj8 5dja 5djc 5djd 5djx 5djy 5djz 5dk0 5dk2 5dvk 5dvl 5dvm 5dvn 5dvo 5gsq 5hsf 5hy9 5hye 5hyf 5hyi 5iq7 5iq9 5iw3 5iw6 5jih 5jii 5jik 5k8d 5kwg 5m3v 5v43 5v4e

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5K33)