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(-) Description

Title :  CRYSTAL STRUCTURE OF FAB DX-2930 IN COMPLEX WITH HUMAN PLASMA KALLIKREIN AT 2.1 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 :  2.10
Chains :  Asym. Unit :  A,B,H,L,M,N
Biol. Unit 1:  A,H,L  (1x)
Biol. Unit 2:  B,M,N  (1x)
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, B
    EC Number: 3.4.21.34
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    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, M
    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, N
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABHLMN
Biological Unit 1 (1x): A HL  
Biological Unit 2 (1x):  B  MN

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:401 , TRP A:518 , LYS A:537BINDING SITE FOR RESIDUE EDO A 701
2AC2SOFTWAREGLU A:479 , GLY A:480 , TYR A:555 , LYS A:556 , VAL H:103BINDING SITE FOR RESIDUE EDO A 702
3AC3SOFTWAREGLN L:37 , PRO L:59 , PHE L:62 , HOH L:411 , HOH L:485BINDING SITE FOR RESIDUE EDO L 301

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:419 -A:435
2A:517 -A:584
3A:548 -A:563
4A:574 -A:602
5B:419 -B:435
6B:517 -B:584
7B:548 -B:563
8B:574 -B:602
9H:22 -H:96
10H:149 -H:205
11L:23 -L:88
12L:133 -L:193
13M:22 -M:96
14M:149 -M:205
15N:23 -N:88
16N:133 -N:193

(-) Cis Peptide Bonds  (8, 8)

Asymmetric 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
5Phe M:155 -Pro M:156
6Glu M:157 -Pro M:158
7Ser N:7 -Pro N:8
8Tyr N:139 -Pro N:140

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OGY)

(-) 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:239
                                                                                                                                                                                                                                                                               
               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...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogy A 391 IVGGTESSWGEWPWQVSLQVKLTAQRHLCGGSLIGHQWVLTAAHCFDGLPLQDVWRIYSGILELSDITKDTPFSQIKEIIIHQNYKVSEGNHDIALIKLQAPLEYTEFQKPISLPSKGDTSTIYTNCWVTGWGFSKEKGEIQNILQKVNIPLVTNEECQKRYQDYKITQRMVCAGYKEGGKDACKGDSGGPLVCKHNGMWRLVGITSWGEGCARREQPGVYTKVAEYMDWILEKTQSSD 629
                                   400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620         


Chain B from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeeee...eeeeeeeeeee..eeeehhhhhh...hhh.eeeee...hhhhh........eeeeee.............eeeee................hhhhhhh....eeeee..............eeee..eehhhhhhhh.........eeee................eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogy B 391 IVGGTESSWGEWPWQVSLQVKLTAQRHLCGGSLIGHQWVLTAAHCFDGLPLQDVWRIYSGILELSDITKDTPFSQIKEIIIHQNYKVSEGNHDIALIKLQAPLEYTEFQKPISLPSKGDTSTIYTNCWVTGWGFSKEKGEIQNILQKVNIPLVTNEECQKRYQDYKITQRMVCAGYKEGGKDACKGDSGGPLVCKHNGMWRLVGITSWGEGCARREQPGVYTKVAEYMDWILEKTQSSD 629
                                   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:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee......eeeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeee.........eee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogy H   1 EVQLLESGGGLVQPGGSLRLSCAASGFTFSHYIMMWVRQAPGKGLEWVSGIYSSGGITVYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAYRRIGVPRRDEFDIWGQGTMVTVSSASTKGPSVFPLAPSSKGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK 223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       144       154       164       174       184       194       204       214         
                                                                                                                                                                   138|                                                                                
                                                                                                                                                                    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..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogy 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  


Chain M from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eee.....eeeeeeee..eeeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeee.........eee...eeeee........eeeee...eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee.eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogy M   2 VQLLESGGGLVQPGGSLRLSCAASGHYIMMWVRQAPGKGLEWVSGIYSSGGITVYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAYRRIGVPRRDEFDIWGQGTMVTVSSASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVYICNVNHKPSNTKVDKRVEP 222
                                    11        21    ||  35        45        55        65        75        85        95       105       115       125       135|      153       163       173       183       193|      212       222
                                                   26|                                                                                                     135|                                              193|                   
                                                    31                                                                                                      144                                               203                   


Chain N 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..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogy N   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 4OGY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

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 Related Entries

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

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

2any PKAL BOUND TO BENZAMIDINE
4ogx PKAL BOUND TO FAB DX-2930 IN DIFFERENT CRYSTAL FORM