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(-) Description

Title :  CRYSTAL STRUCTURE OF FAB DX-2930 IN COMPLEX WITH HUMAN PLASMA KALLIKREIN AT 2.4 ANGSTROM RESOLUTION
 
Authors :  T. E. Edwards, M. C. Clifton, J. Abendroth, A. Nixon, R. Ladner
Date :  16 Jan 14  (Deposition) - 09 Jul 14  (Release) - 10 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Fab, Antibody, Kallikrein, Blood, Plasma, Plasma Kallikrein- Mediated Edema, Acute Hereditary Angioedema, Hae, Hmwk, Serpin C1-Inhibitor, C1-Inh, Hereditary Angioedema, Haw, Bradykinin, Fletcher Factor, Kininogenin, Serine Protease, Edema, Hydrolase-Antibody Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Kenniston, R. R. Faucette, D. Martik, S. R. Comeau, A. P. Lindberg K. J. Kopacz, G. P. Conley, J. Chen, M. Viswanathan, N. Kastrapeli, J. Cosic, S. Mason, M. Dileo, J. Abendroth, P. Kuzmic, R. C. Ladner, T. E. Edwards, C. Tenhoor, B. A. Adelman, A. E. Nixon, D. J. Sexton
Inhibition Of Plasma Kallikrein By A Highly Specific Active Site Blocking Antibody.
J. Biol. Chem. V. 289 23596 2014
PubMed-ID: 24970892  |  Reference-DOI: 10.1074/JBC.M114.569061

(-) Compounds

Molecule 1 - PLASMA KALLIKREIN
    Chains: A
    EC Number: 3.4.21.34
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 391-631
    Gene: KLK3, KLKB1, KLKB1_HUMAN
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: FLETCHER FACTOR, KININOGENIN, PLASMA PREKALLIKREIN, PLASMA KALLIKREIN HEAVY CHAIN, PLASMA KALLIKREIN LIGHT CHAIN
 
Molecule 2 - DX-2930 HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - DX-2930 LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    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  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:425 , HIS A:426 , GLN A:427 , TRP A:428BINDING SITE FOR RESIDUE SO4 A 701
2AC2SOFTWAREGLN A:549 , GLN A:553 , TYR A:555 , HOH A:881 , HOH A:898BINDING SITE FOR RESIDUE SO4 A 702
3AC3SOFTWAREHIS A:472 , GLN A:473 , ARG A:560BINDING SITE FOR RESIDUE SO4 A 703
4AC4SOFTWARETHR A:515 , HIS A:586 , HOH A:832BINDING SITE FOR RESIDUE SO4 A 704
5AC5SOFTWARETHR A:544 , ASN A:545 , HOH A:826 , HOH A:908 , HOH A:909BINDING SITE FOR RESIDUE SO4 A 705
6AC6SOFTWAREARG A:551BINDING SITE FOR RESIDUE SO4 A 706

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:419 -A:435
2A:517 -A:584
3A:548 -A:563
4A:574 -A:602
5H:22 -H:96
6H:149 -H:205
7L:23 -L:88
8L:133 -L:193

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe H:155 -Pro H:156
2Glu H:157 -Pro H:158
3Ser L:7 -Pro L:8
4Tyr L:139 -Pro L:140

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OGX)

(-) 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:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeeee...eeeeeeeeeee..eeeehhhhhh...hhh.eeee....hhhhh........eeeeee.............eeeee................hhhhh......eeeee..............eeee..eehhhhhhhh.........eeee................eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogx A 391 IVGGTESSWGEWPWQVSLQVKLTAQRHLCGGSLIGHQWVLTAAHCFDGLPLQDVWRIYSGILELSDITKDTPFSQIKEIIIHQNYKVSEGNHDIALIKLQAPLEYTEFQKPISLPSKGDTSTIYTNCWVTGWGFSKEKGEIQNILQKVNIPLVTNEECQKRYQDYKITQRMVCAGYKEGGKDACKGDSGGPLVCKHNGMWRLVGITSWGEGCARREQPGVYTKVAEYMDWILEKTQ 626
                                   400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620      


Chain H from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee......eeeeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeee.........eee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ogx H   1 EVQLLESGGGLVQPGGSLRLSCAASGFTFSHYIMMWVRQAPGKGLEWVSGIYSSGGITVYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAYRRIGVPRRDEFDIWGQGTMVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     ||146       156       166       176       186       196       206       216      
                                                                                                                                                                 136|                                                                               
                                                                                                                                                                  143                                                                               


Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogx L   1 DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYKASTLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQYNTYWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 4OGX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Tyr L:139 - Pro L:140   [ RasMol ]  
 

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  KLKB1_HUMAN | P03952
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 Related Entries

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

UniProtKB/Swiss-Prot
        KLKB1_HUMAN | P03952: 2anw 2any 4ogy 5f8t 5f8x 5f8z 5tjx
UniProtKB/TrEMBL
        Q7Z3Y4_HUMAN | Q7Z3Y4: 1axs 1l7i 1pg7 1s78 2jix 4ogy 4pub
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(-) Related Entries Specified in the PDB File

2any PKAL BOUND TO BENZAMIDINE
4ogy