PDBsum entry 1zv5

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Hydrolase/immune system PDB id
Protein chains
129 a.a. *
119 a.a. *
PO4 ×2
Waters ×46
* Residue conservation analysis
PDB id:
Name: Hydrolase/immune system
Title: Crystal structure of the variable domain of the camelid heavy-chain antibody d2-l29 in complex with hen egg white lysozyme
Structure: LysozymE C. Chain: l. Synonym: 1,4-beta-n-acetylmuramidasE C, allergen gal d 4, gal d iv. Immunoglobulin heavy chain antibody variable domain. Chain: a. Fragment: vhh d2-l29. Engineered: yes
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Camelus dromedarius. Arabian camel. Organism_taxid: 9838. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
2.00Å     R-factor:   0.217     R-free:   0.239
Authors: E.De Genst,K.Silence,K.Decanniere,K.Conrath,R.Loris,J.Kinne, S.Muyldermans,L.Wyns
Key ref:
E.De Genst et al. (2006). Molecular basis for the preferential cleft recognition by dromedary heavy-chain antibodies. Proc Natl Acad Sci U S A, 103, 4586-4591. PubMed id: 16537393 DOI: 10.1073/pnas.0505379103
01-Jun-05     Release date:   04-Apr-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00698  (LYSC_CHICK) -  Lysozyme C
147 a.a.
129 a.a.
Protein chain
No UniProt id for this chain
Struc: 119 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain L: E.C.  - Lysozyme.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     6 terms  


DOI no: 10.1073/pnas.0505379103 Proc Natl Acad Sci U S A 103:4586-4591 (2006)
PubMed id: 16537393  
Molecular basis for the preferential cleft recognition by dromedary heavy-chain antibodies.
E.De Genst, K.Silence, K.Decanniere, K.Conrath, R.Loris, J.Kinne, S.Muyldermans, L.Wyns.
Clefts on protein surfaces are avoided by antigen-combining sites of conventional antibodies, in contrast to heavy-chain antibodies (HCAbs) of camelids that seem to be attracted by enzymes' substrate pockets. The explanation for this pronounced preference of HCAbs was investigated. Eight single domain antigen-binding fragments of HCAbs (VHH) with nanomolar affinities for lysozyme were isolated from three immunized dromedaries. Six of eight VHHs compete with small lysozyme inhibitors. This ratio of active site binders is also found within the VHH pool derived from polyclonal HCAbs purified from the serum of the immunized dromedary. The crystal structures of six VHHs in complex with lysozyme and their interaction surfaces were compared to those of conventional antibodies with the same antigen. The interface sizes of VHH and conventional antibodies to lysozyme are very similar as well as the number and chemical nature of the contacts. The main difference comes from the compact prolate shape of VHH that presents a large convex paratope, predominantly formed by the H3 loop and interacting, although with different structures, into the concave lysozyme substrate-binding pocket. Therefore, a single domain antigen-combining site has a clear structural advantage over a conventional dimeric format for targeting clefts on antigenic surfaces.
  Selected figure(s)  
Figure 1.
Fig. 1. Epitope mapping of the monoclonal and polyclonal VHHs. (A) HEWL binding of all VHHs in the presence of a saturating concentration of cAb-Lys-3 using a coinjection procedure. (B) Epitopes of HEWL active site binders based on the inhibition of binding by NAG3 and Biebrich Scarlet. (C) Residual HEWL binding of polyclonal VHH derived from the IgG3 fraction of dromedary D2. (Left) Binding in absence of competitor (set at 100%). (Center) Binding in presence of HEWL-saturating concentrations of D2-L24. (Right) Binding in presence of HEWL-saturating concentrations of D2-L19.
Figure 3.
Fig. 3. Superposition of the antibody-lysozyme complexes for conventional antibodies (Left) and for VHHs (Right). The HEWL molecules (gray surfaces) are shown in the same orientation for both antibody classes. The antibody molecules are represented as colored ribbons and their identity is indicated in the same color.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21244216 F.Rahbarizadeh, D.Ahmadvand, and Z.Sharifzadeh (2011).
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21450996 L.I.Ibañez, M.De Filette, A.Hultberg, T.Verrips, N.Temperton, R.A.Weiss, W.Vandevelde, B.Schepens, P.Vanlandschoot, and X.Saelens (2011).
Nanobodies with in vitro neutralizing activity protect mice against H5N1 influenza virus infection.
  J Infect Dis, 203, 1063-1072.  
21219561 O.Zafra, S.Fraile, C.Gutiérrez, A.Haro, A.D.Páez-Espino, J.I.Jiménez, and Lorenzo (2011).
Monitoring biodegradative enzymes with nanobodies raised in Camelus dromedarius with mixtures of catabolic proteins.
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21557949 P.J.Aston, G.Derks, A.Raji, B.M.Agoram, and P.H.van der Graaf (2011).
Mathematical analysis of the pharmacokinetic-pharmacodynamic (PKPD) behaviour of monoclonal antibodies: Predicting in vivo potency.
  J Theor Biol, 281, 113-121.  
20140750 A.Van den Abbeele, S.De Clercq, A.De Ganck, V.De Corte, B.Van Loo, S.H.Soror, V.Srinivasan, J.Steyaert, J.Vandekerckhove, and J.Gettemans (2010).
A llama-derived gelsolin single-domain antibody blocks gelsolin-G-actin interaction.
  Cell Mol Life Sci, 67, 1519-1535.
PDB codes: 2x1o 2x1p 2x1q
20458517 D.Smolarek, C.Hattab, G.Hassanzadeh-Ghassabeh, S.Cochet, C.Gutiérrez, Brevern, R.Udomsangpetch, J.Picot, M.Grodecka, K.Wasniowska, S.Muyldermans, Y.Colin, C.Le Van Kim, M.Czerwinski, and O.Bertrand (2010).
A recombinant dromedary antibody fragment (VHH or nanobody) directed against human Duffy antigen receptor for chemokines.
  Cell Mol Life Sci, 67, 3371-3387.  
19796917 F.Scheuplein, B.Rissiek, J.P.Driver, Y.G.Chen, F.Koch-Nolte, and D.V.Serreze (2010).
A recombinant heavy chain antibody approach blocks ART2 mediated deletion of an iNKT cell population that upon activation inhibits autoimmune diabetes.
  J Autoimmun, 34, 145-154.  
20138889 J.Dong, A.A.Thompson, Y.Fan, J.Lou, F.Conrad, M.Ho, M.Pires-Alves, B.A.Wilson, R.C.Stevens, and J.D.Marks (2010).
A single-domain llama antibody potently inhibits the enzymatic activity of botulinum neurotoxin by binding to the non-catalytic alpha-exosite binding region.
  J Mol Biol, 397, 1106-1118.
PDB code: 3k3q
20098614 J.O.Conway, L.J.Sherwood, M.T.Collazo, J.A.Garza, and A.Hayhurst (2010).
Llama single domain antibodies specific for the 7 botulinum neurotoxin serotypes as heptaplex immunoreagents.
  PLoS One, 5, e8818.  
20093370 J.Thanongsaksrikul, P.Srimanote, S.Maneewatch, K.Choowongkomon, P.Tapchaisri, S.Makino, H.Kurazono, and W.Chaicumpa (2010).
A V H H that neutralizes the zinc metalloproteinase activity of botulinum neurotoxin type A.
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20616002 L.Deng, C.A.Velikovsky, G.Xu, L.M.Iyer, S.Tasumi, M.C.Kerzic, M.F.Flajnik, L.Aravind, Z.Pancer, and R.A.Mariuzza (2010).
A structural basis for antigen recognition by the T cell-like lymphocytes of sea lamprey.
  Proc Natl Acad Sci U S A, 107, 13408-13413.
PDB codes: 3m18 3m19
20843201 L.Huang, S.Muyldermans, and D.Saerens (2010).
Nanobodies®: proficient tools in diagnostics.
  Expert Rev Mol Diagn, 10, 777-785.  
20945358 M.H.Kubala, O.Kovtun, K.Alexandrov, and B.M.Collins (2010).
Structural and thermodynamic analysis of the GFP:GFP-nanobody complex.
  Protein Sci, 19, 2389-2401.
PDB code: 3ogo
20482318 R.A.Mariuzza, C.A.Velikovsky, L.Deng, G.Xu, and Z.Pancer (2010).
Structural insights into the evolution of the adaptive immune system: the variable lymphocyte receptors of jawless vertebrates.
  Biol Chem, 391, 753-760.  
20704569 R.Ganesan, C.Eigenbrot, and D.Kirchhofer (2010).
Structural and mechanistic insight into how antibodies inhibit serine proteases.
  Biochem J, 430, 179-189.  
20975043 S.Hubert, B.Rissiek, K.Klages, J.Huehn, T.Sparwasser, F.Haag, F.Koch-Nolte, O.Boyer, M.Seman, and S.Adriouch (2010).
Extracellular NAD+ shapes the Foxp3+ regulatory T cell compartment through the ART2-P2X7 pathway.
  J Exp Med, 207, 2561-2568.  
21059953 S.Jähnichen, C.Blanchetot, D.Maussang, M.Gonzalez-Pajuelo, K.Y.Chow, L.Bosch, S.De Vrieze, B.Serruys, H.Ulrichts, W.Vandevelde, M.Saunders, H.J.De Haard, D.Schols, R.Leurs, P.Vanlandschoot, T.Verrips, and M.J.Smit (2010).
CXCR4 nanobodies (VHH-based single variable domains) potently inhibit chemotaxis and HIV-1 replication and mobilize stem cells.
  Proc Natl Acad Sci U S A, 107, 20565-20570.  
19889627 S.P.Adekar, I.Klyubin, S.Macy, M.J.Rowan, A.Solomon, S.K.Dessain, and B.O'Nuallain (2010).
Inherent anti-amyloidogenic activity of human immunoglobulin gamma heavy chains.
  J Biol Chem, 285, 1066-1074.  
20400507 W.W.Koh, S.Steffensen, M.Gonzalez-Pajuelo, B.Hoorelbeke, A.Gorlani, A.Szynol, A.Forsman, M.M.Aasa-Chapman, Haard, T.Verrips, and R.A.Weiss (2010).
Generation of a family-specific phage library of llama single chain antibody fragments that neutralize HIV-1.
  J Biol Chem, 285, 19116-19124.  
19862637 Y.H.Teh, and T.A.Kavanagh (2010).
High-level expression of Camelid nanobodies in Nicotiana benthamiana.
  Transgenic Res, 19, 575-586.  
19196718 A.Monegal, D.Ami, C.Martinelli, H.Huang, M.Aliprandi, P.Capasso, C.Francavilla, G.Ossolengo, and Marco (2009).
Immunological applications of single-domain llama recombinant antibodies isolated from a naïve library.
  Protein Eng Des Sel, 22, 273-280.  
19543291 C.A.Velikovsky, L.Deng, S.Tasumi, L.M.Iyer, M.C.Kerzic, L.Aravind, Z.Pancer, and R.A.Mariuzza (2009).
Structure of a lamprey variable lymphocyte receptor in complex with a protein antigen.
  Nat Struct Mol Biol, 16, 725-730.
PDB codes: 3g39 3g3a 3g3b
19531051 G.Behar, P.Chames, I.Teulon, A.Cornillon, F.Alshoukr, F.Roquet, M.Pugnière, J.L.Teillaud, A.Gruaz-Guyon, A.Pèlegrin, and D.Baty (2009).
Llama single-domain antibodies directed against nonconventional epitopes of tumor-associated carcinoembryonic antigen absent from nonspecific cross-reacting antigen.
  FEBS J, 276, 3881-3893.  
19529959 J.Wesolowski, V.Alzogaray, J.Reyelt, M.Unger, K.Juarez, M.Urrutia, A.Cauerhff, W.Danquah, B.Rissiek, F.Scheuplein, N.Schwarz, S.Adriouch, O.Boyer, M.Seman, A.Licea, D.V.Serreze, F.A.Goldbaum, F.Haag, and F.Koch-Nolte (2009).
Single domain antibodies: promising experimental and therapeutic tools in infection and immunity.
  Med Microbiol Immunol, 198, 157-174.  
19561045 L.S.Matheson, M.J.Osborn, J.A.Smith, D.Corcos, M.Hamon, R.Chaouaf, J.Coadwell, G.Morgan, D.Oxley, and M.Brüggemann (2009).
Light chain-deficient mice produce novel multimeric heavy-chain-only IgA by faulty class switching.
  Int Immunol, 21, 957-966.  
19501012 M.Gebauer, and A.Skerra (2009).
Engineered protein scaffolds as next-generation antibody therapeutics.
  Curr Opin Chem Biol, 13, 245-255.  
  19298050 S.Koide, and S.S.Sidhu (2009).
The importance of being tyrosine: lessons in molecular recognition from minimalist synthetic binding proteins.
  ACS Chem Biol, 4, 325-334.  
19477632 S.Koide (2009).
Engineering of recombinant crystallization chaperones.
  Curr Opin Struct Biol, 19, 449-457.  
18842738 A.Forsman, E.Beirnaert, M.M.Aasa-Chapman, B.Hoorelbeke, K.Hijazi, W.Koh, V.Tack, A.Szynol, C.Kelly, A.McKnight, T.Verrips, Haard, and R.A.Weiss (2008).
Llama antibody fragments with cross-subtype human immunodeficiency virus type 1 (HIV-1)-neutralizing properties and high affinity for HIV-1 gp120.
  J Virol, 82, 12069-12081.  
18445649 J.Huang, A.Koide, K.Makabe, and S.Koide (2008).
Design of protein function leaps by directed domain interface evolution.
  Proc Natl Acad Sci U S A, 105, 6578-6583.
PDB code: 2qbw
18632867 L.Garaicoechea, A.Olichon, G.Marcoppido, A.Wigdorovitz, M.Mozgovoj, L.Saif, T.Surrey, and V.Parreño (2008).
Llama-derived single-chain antibody fragments directed to rotavirus VP6 protein possess broad neutralizing activity in vitro and confer protection against diarrhea in mice.
  J Virol, 82, 9753-9764.  
18297364 L.Huang, L.O.Gainkam, V.Caveliers, C.Vanhove, M.Keyaerts, P.De Baetselier, A.Bossuyt, H.Revets, and T.Lahoutte (2008).
SPECT imaging with 99mTc-labeled EGFR-specific nanobody for in vivo monitoring of EGFR expression.
  Mol Imaging Biol, 10, 167-175.  
18602117 R.N.Gilbreth, K.Esaki, A.Koide, S.S.Sidhu, and S.Koide (2008).
A dominant conformational role for amino acid diversity in minimalist protein-protein interfaces.
  J Mol Biol, 381, 407-418.
PDB codes: 3csb 3csg
17420456 A.Koide, R.N.Gilbreth, K.Esaki, V.Tereshko, and S.Koide (2007).
High-affinity single-domain binding proteins with a binary-code interface.
  Proc Natl Acad Sci U S A, 104, 6632-6637.
PDB code: 2obg
17888451 A.Koide, V.Tereshko, S.Uysal, K.Margalef, A.A.Kossiakoff, and S.Koide (2007).
Exploring the capacity of minimalist protein interfaces: interface energetics and affinity maturation to picomolar KD of a single-domain antibody with a flat paratope.
  J Mol Biol, 373, 941-953.
PDB codes: 2p49 2p4a
17257422 A.Olichon, D.Schweizer, S.Muyldermans, and Marco (2007).
Heating as a rapid purification method for recovering correctly-folded thermotolerant VH and VHH domains.
  BMC Biotechnol, 7, 7.  
18042730 G.Habicht, C.Haupt, R.P.Friedrich, P.Hortschansky, C.Sachse, J.Meinhardt, K.Wieligmann, G.P.Gellermann, M.Brodhun, J.Götz, K.J.Halbhuber, C.Röcken, U.Horn, and M.Fändrich (2007).
Directed selection of a conformational antibody domain that prevents mature amyloid fibril formation by stabilizing Abeta protofibrils.
  Proc Natl Acad Sci U S A, 104, 19232-19237.  
17195019 M.J.Taussig, O.Stoevesandt, C.A.Borrebaeck, A.R.Bradbury, D.Cahill, C.Cambillau, Daruvar, S.Dübel, J.Eichler, R.Frank, T.J.Gibson, D.Gloriam, L.Gold, F.W.Herberg, H.Hermjakob, J.D.Hoheisel, T.O.Joos, O.Kallioniemi, M.Koegl, M.Koegll, Z.Konthur, B.Korn, E.Kremmer, S.Krobitsch, U.Landegren, S.van der Maarel, J.McCafferty, S.Muyldermans, P.A.Nygren, S.Palcy, A.Plückthun, B.Polic, M.Przybylski, P.Saviranta, A.Sawyer, D.J.Sherman, A.Skerra, M.Templin, M.Ueffing, and M.Uhlén (2007).
ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome.
  Nat Methods, 4, 13-17.  
17512622 M.Jain, N.Kamal, and S.K.Batra (2007).
Engineering antibodies for clinical applications.
  Trends Biotechnol, 25, 307-316.  
17704915 M.M.Harmsen, and H.J.De Haard (2007).
Properties, production, and applications of camelid single-domain antibody fragments.
  Appl Microbiol Biotechnol, 77, 13-22.  
18074396 R.L.Rich, and D.G.Myszka (2007).
Survey of the year 2006 commercial optical biosensor literature.
  J Mol Recognit, 20, 300-366.  
17291278 Y.H.Chien, and Y.Konigshofer (2007).
Antigen recognition by gammadelta T cells.
  Immunol Rev, 215, 46-58.  
18077410 Y.Wu, C.Eigenbrot, W.C.Liang, S.Stawicki, S.Shia, B.Fan, R.Ganesan, M.T.Lipari, and D.Kirchhofer (2007).
Structural insight into distinct mechanisms of protease inhibition by antibodies.
  Proc Natl Acad Sci U S A, 104, 19784-19789.
PDB codes: 2r0k 2r0l
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