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(-) Description

Title :  DUAL-SPECIFICITY FAB 5A12 IN COMPLEX WITH ANGIOPOIETIN 2
 
Authors :  S. F. Harris, P. Wu
Date :  21 Apr 15  (Deposition) - 01 Jul 15  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Fab, Daf, Angiogenesis, Tie Receptor, Signaling Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Koenig, C. V. Lee, S. Sanowar, P. Wu, J. Stinson, S. F. Harris, G. Fuh
Deep Sequencing-Guided Design Of A High Affinity Dual Specificity Antibody To Target Two Angiogenic Factors In Neovascular Age-Related Macular Degeneration.
J. Biol. Chem. V. 290 21773 2015
PubMed-ID: 26088137  |  Reference-DOI: 10.1074/JBC.M115.662783

(-) Compounds

Molecule 1 - ANGIOPOIETIN-2
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Fragment: RECEPTOR BINDING DOMAIN, UNP RESIDUES 225-444
    Gene: ANGPT2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ANG-2
 
Molecule 2 - FRAGMENT ANTIGEN BINDING 5A12 HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - FRAGMENT ANTIGEN BINDING 5A12 LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2SO44Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:429 , ASP A:431 , CYS A:433 , CYS A:435 , HOH A:707 , HOH A:730binding site for residue CA A 601
2AC2SOFTWARELYS A:473 , TYR A:475 , SER A:480 , GLY A:481 , HOH A:702 , HOH A:783 , PHE L:27A , SER L:30 , HOH L:303binding site for residue SO4 A 602
3AC3SOFTWAREARG A:337 , PHE A:346 , GLY A:347binding site for residue SO4 A 603
4AC4SOFTWAREGLY A:405 , LEU A:406 , LYS L:145binding site for residue SO4 A 604
5AC5SOFTWAREARG H:19 , LYS H:75 , TYR H:79 , HOH H:413 , HOH H:431 , HOH H:468 , HOH H:500binding site for residue SO4 H 301

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:284 -A:313
2A:433 -A:435
3A:437 -A:450
4H:22 -H:92
5H:140 -H:196
6L:23 -L:88
7L:134 -L:194

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Gln A:418 -Pro A:419
2Ala A:449 -Cys A:450
3Leu H:99 -Pro H:100
4Phe H:146 -Pro H:147
5Glu H:148 -Pro H:149
6Ser L:7 -Pro L:8
7Ser L:94 -Pro L:95
8Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZFG)

(-) 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:220
                                                                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhh.....eeeeee......eeeeeee.hhhhh.eeeeeee.........hhhhhhhhee.....ee.hhhhhhhhhhhh.eeeeeeee.....eeeeeeeeeee.hhhhh..eeeeeeee...........................hhhhhhh..........ee..................eehhhhh......eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4zfg A  278 QISFRDCAEVFKSGHTTNGIYTLTFPNSTEEIKAYCDMEAGGGGWTIIQRREDGSVDFQRTWKEYKVGFGNPSGEYWLGNEFVSQLTNQQRYVLKIHLKDWEGNEAYSLYEHFYLSSEELNYRIHLKGLTGTAGKISSISQPGNDFSTKDGDNDKCICKCSQMLTGGWWFDACGPSNLNGMYYPQRQNTNKFNGIKWYYWKGSGYSLKATTMMIRPADFG  497
                                   287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497


Chain H from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeee......eeeeeee....eeee.......eeeeee....eeeeee...hhhhheeeeeeee.......eeee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4zfg H    1 EVQLVESGGGLVQPGGSLRLSCAASGFTISDYWIHWVRQAPGKGLEWVAGITPAGGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARFVFFLPYAMDYWGQGTLVTVSSASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVE  212
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123    || 137       147       157       167       177       187       197       207     
                                                                              52A                            82A||               100A||                         128|                                                                               
                                                                                                              82B|                100B|                          133                                                                               
                                                                                                               82C                 100C                                                                                                            


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeeeeeeehhh.eeeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhheeeeeee...........eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4zfg L    1 DIQMTQSPSSLSASVGDRVTITCRASQFLSSFGVAWYQQKPGKAPKLLIYGASSLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQGLLSPLTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    10        20       |29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209   
                                                     27A
   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 4ZFG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:449 - Cys A:450   [ RasMol ]  
    Gln A:418 - Pro A:419   [ RasMol ]  
    Glu H:148 - Pro H:149   [ RasMol ]  
    Leu H:99 - Pro H:100   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Ser L:94 - Pro L:95   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        ANGP2_HUMAN | O15123: 1z3s 1z3u 2gy7 4jzc

(-) Related Entries Specified in the PDB File

4zff