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Antibody 3D structures

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Revision as of 07:22, 9 October 2022 by Michal Harel (Talk | contribs)
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Humanized mouse antibody (hmFab) is a modified mFab which resembles more hFab.
Broadly neutralizing Fab and Neutralizing Fab are anti-HIV Fab.
Lama antibodies or nanobodies or camelid or VHH are natural single-domain antibodies containing just the heavy chain.
scFv is a single chain variable fragment in a fusion protein of the variable regions of the heavy and light chains of immunoglobulin.

3D structures of Antibody

Updated on 09-October-2022 {{#tree:id=OrganizedByTopic|openlevels=0|


  • Fab
  • Anti-HIV Fab or broadly neutralizing Fab
  • Anti-SARS-CoV-2 Fab
  • Anti-MERS-CoV Fab
    • 6nb5 - hFab anti-MERS-CoV
    • 6pxg - mFab anti-MERS-CoV
    • 7coe - hFab + MERS-CoV spike protein
    • 6nb3, 6nb4, 7v5k, 7v6n - hFab + MERS-CoV spike protein – Cryo EM
    • 6pxh, 6pz8, 7s3m - mFab anti-MERS-CoV + MERS-CoV protein
    • 6j11 - mscFv + MERS-CoV spike protein
    • 6war - LgVHH + MERS-CoV spike protein
  • Anti-hepatitis Fab


  • Human Fab: small molecule complex
  • Mouse Fab: small molecule complex
  • Other Fab: small molecule complex
    • 2jb5, 2jb6 - hmFab + hapten
    • 3eyv - hmFab 13G5 (mutant) + hapten
  • Mouse Fab: peptide complex
    • 3e8u - mFab + BNP peptide
    • 2a6d, 2a6i, 2a6j, 2a6k - mFab + peptide
    • 3hr5 – mFab + M1prime peptide
    • 3eys, 3eyu - mFab + amyloid-β-related peptide
    • 3ggw – mFab + carbohydrate-mimetic peptide
    • 3cxd, 3dsf, 5x5x – mFab + osteopontin peptide
    • 2zpk – mFab + proteinase-activated receptor peptide
    • 3ifl, 3ifn, 3ifo, 3ifp, 7e6p - mFab + amyloid peptide
    • 2eh8 - mFab + PRES1 peptide
    • 2brr – mFab + outer membrane protein peptide
    • 1xgy, 7doh – mFab + rhodopsin peptide
    • 1pz5 – mFab SYA/J6 + peptide
    • 1a3r – mFab + rhinovirus capsid peptide
    • 1cu4 - mFab + prion protein peptide
    • 1fpt – mFab + poliovirus peptide
    • 1mvu – mFab + glycoprotein
    • 2ap2 – mFab + glycoprotein peptide + C-myc peptide
    • 1frg, 1him, 1hin, 1ifh - mFab + hemagglutinin peptide
    • 1tet – mFab + cholera toxin peptide
    • 5epm – mFab + therapotoxin peptide
    • 1i8i, 1i8k – mFab + EGFR peptide
    • 4gag, 4gaj – mFab + genome polyprotein peptide
    • 5mv4, 5mu0 – mFab + collagen peptide
    • 6f7t – mFab + RNase peptide
    • 7njz, 7nw3 – mFab + chemokine receptor peptide
    • 7v4w, 7v64, 7v7k, 7v8q, 7vac, 7vaz – mFab + mucin peptide
    • 7o2z, 7o30, 7o31, 7o33 – mFab + PAS peptide
    • 7fgj, 7fgl, 7fgr - mFab + Tau peptide
  • Human Fab: peptide complex
  • Other Fab: peptide complex
    • 2hh0 – hmFab + prion protein peptide
    • 3bky – hmFab + CD20 peptide
    • 5dmg – rFab + microtubule-associated protein peptide
    • 6ldy, 6x1s, 6x1t, 6x1u, 6x1v, 6x1w – rFab + peptide
    • 5dd0 – rmFab + peptide
    • 6df1, 6df2 - syFab anti-phosphotyrosine + phosphotyrosine peptide
  • Anti-HIV Fab: peptide complex
  • Human Fab: protein complex
  • Human Fab: viral protein complex
    • 4dag, 7sem – hFab + metapneumovirus glycoprotein F0
    • 7tl0, 8cw9 – hFab + metapneumovirus glycoprotein F0 – Cryo EM
    • 6p91, 6p95, 7s8h – hFab + lassa virus glycoprotein
    • 7tyv, 7uds, 7ul7 – hFab + lassa virus glycoprotein – Cryo EM
    • 7t4s – hFab + HCMV glycoprotein – Cryo EM
    • 7l7r – hFab + hemorrhagic fever virus glycoprotein
    • 6yo6 – hFab + LgHC3NB1
    • 7jie – hFab + norovirus VP1
    • 6gv4 – hFab + parechovirus proteins + RNA - Cryo EM
    • 7d5z, 7kbb – hFab + herpesvirus proteins
    • 6c5v, 7fbi, 7kdd, 7lbe, 7lbf, 7lbg, 7m30, 7t4q, 7t4r – hFab + herpesvirus proteins - Cryo EM
    • 6b9j – syFab + vaccinia virus protein
    • 6otc – syFab + Marburg virus protein
    • 6svl – syFab + MYDGF
    • 7mmn – Fab + Escherichia virus protein
  • Mouse Fab: protein complex
  • Mouse Fab: viral protein complex
    • 6a0z, 1eo8, 1ken, 4mhh, 4mhj, 6n5b, 6n5d - mFab anti-influenza virus hemagglutinin
    • 4qnp, 1nca, 1ncb, 1ncc, 1ncd – mFab + influenza neuraminidase
    • 6n5e, 7fah – mFab + influenza hemagglutinin
    • 6wzt, 7dkj, 7jix, 7yhk – mFab + influenza hemagglutinin – Cryo EM
    • 1rvf – mFab 17-IA + intact rhinovirus
    • 3j3o, 3j3p- mFab + poliovirus proteins – cryoEM
    • 6mui, 6mw9, 6mwc, 6mwv, 6mwx - mFab + equine encephalitis virus proteins – cryoEM
    • 5kvg, 5kvf, 5kve, 5kvd, 5jhl, 6uta – mFab + zika envelope DIII
    • 3ve0 - mFab + Ebola envelope glycoprotein
    • 5y9t, 5y9c, 5y9f, 7ew5 – mFab + papilloma virus capsid protein
    • 4l5f, 6fla, 6flb, 6flc – mFab + dengue virus envelope protein
    • 5zud, 5zuf, 6aj7, 6aj9 – mFab + enterovirus caspid proteins – Cryo EM
    • 3fmg – mFab + rotavirus glycoprotein VP7
    • 3ixx, 3ixy - mFab E53 + envelope glycoprotein + West Nile virus peptide
    • 7ki6 – mFab + Hendra virus F0 – Cryo EM
    • 7ki4, 7txz, 7ty0 – mFab + nipah virus protein – Cryo EM
    • 7rfp – mFab + muromegalovirus GITR – Cryo EM
    • 7u9g, 8a1e – mFab + rabies virus glycoprotein – Cryo EM
    • 7kyl – mFab + deer tick virus glycoprotein
    • 7c80, 7c81, 7eaj, 7eak, 7cmk – mFab + echovirus glycoproteins – Cryo EM
    • 7m3l, 7m3m, 7m3n – mFab + parvovirus glycoproteins – Cryo EM
    • 7qu1 – mFab + marchupovirus glycoproteins
    • 7qu2 – mFab + mammarenavirus glycoproteins
    • 7dq7 – mFab + coxsackievirus proteins – Cryo EM
  • Anti-HIV Fab: protein complex or broadly neutralizing antibody complex
  • Other Fab: protein complex
    • 3ld8, 3ldb – AhFab + bifunctional arginine demethylase
    • 3mj9 – AhFab HL4E10 + JAML
    • 3r08 - AhFab 2C11 + CD3ε
    • 1jps - hmFab D3H44 + tissue factor
    • 5f3h, 5f3b - hmFab + growth factor 8
    • 1pkq – hmFab 8-18C5 + myelin glycoprotein
    • 2b2x – rFab AQC2 + integrin
    • 4ht1 – rFab + TNF ligand 12
    • 6cf2 – rFab + REV
    • 2r56 – bFab igE + β-lactoglobulin
    • 1g6v – bFab + carbonic anhydrase
    • 7eo0, 7fei, 7fej – bFab + FMD virus proteins – Cryo EM
    • 4n9g - rmFab + scaffold
    • 6xgc – rmFab + Influenza virus hemagglutinin – Cryo EM
    • 7nks, 7nrh, 7o9s - rFab + hantavirus envelope polyprotein
    • 6z06 - vFab + hantavirus envelope polyprotein – vole
    • 7b09 - vFab + hantavirus envelope polyprotein – Cryo EM
    • 6oor – raFab + β-2-microglobulin + CD1D
    • 6e62 – raFab + malaria protein
    • 6qig – raFab + ADAMTS-13
    • 6al0, 6al1 – raFab + S2P
    • 7k22, 7k23 – raFab + VP1 – Cryo EM
    • 7kq7 – raFab + IL21R
    • 6gku – LgFab + galectin
    • 4hgk – Fab + albumin – shark
    • 6vi1 – syFab + terminase
    • 6iap – syFab + Nkp46
    • 7mdj - syFab + KcsA K+ channel + ion
    • 7keo – syFab igG1 + ubiquitin
    • 6i8s - EcFab + plasminogen activator inhibitor – Escherichia coli
    • 6pis – Fab + TRAAK – Cricetulus migratorius
    • 7y7m, 7yms, 7yrf, 7yrh – Fab + coxsackievirus proteins – Cryo EM


  • Human Fab: protein higher complexes
    • 2wuc - hFab 40 + hepatocyte growth factor activator + inhibitor
    • 3d85 - hFab 7G10 + IL-12 + IL-23
    • 4xwo - hFab + ATPase GET3 + Sec22
    • 4xvu - hFab + ATPase GET3 + NYV1
    • 4xtr - hFab + ATPase GET3 + PEP12P peptide
    • 4xmn - hFab + Sec13 + Nup145 + Nup84 + Nup120 + Nup85
    • 4xmm - hFab + Sec13 + Nup145 + Nup84 + Nup120 + Nup85 + SEH1
    • 4mxw - hFab + TNFR-III + lymphotoxin
    • 3bt2 – hFab anti-UPAR + urokinase-type plasminogen activator + vitronectin
    • 6cw2 – hFab + histone acetyltransferase + transcriptional adapter
    • 6c08 – hFab + amino acid transporter + Arg
    • 6apd – hFab + RSV fusion protein + immunoglobulin + IGL
    • 6w51 – hFab + 2-b-microglobulin + MHC + p53 peptide
    • 7bbg – hFab + 2-b-microglobulin + MHC + wilms tumor peptide
    • 3gjf, 3hae – hFab + β-2-microglobulin + MHC antigen + NYESO peptide
    • 7bh8 – hFab + 2-b-microglobulin + MHC + VL9 peptide
    • 6o1f - hFab + trypsin inhibitor + tryptase
    • 7joo - hFab + LgVHH + ICOS
    • 6fn1, 7a65, 7a69, 7a6c, 7a6e, 7a6f – hFab + ABCB + drug
    • 6w9g - hFab + CD40 + fluorescent amino acid
    • 6ww2 – hFab + syVHH + frizzled-5 – Cryo EM
    • 7tdm, 7tdn – hFab + claudin + enterotoxin – Cryo EM
    • 7mhy – hFab + HHAT + palmitoyl-CoA – Cryo EM
    • 7ncs, 7nd0 – hFab in BAM complex – Cryo EM
  • Mouse Fab: protein higher complexes
    • 5w3e, 5w3l, 5w3m, 5w3o, 5w3p - mFab C5 + Rhinovirus protein 1 + protein 2 + protein 3 + protein 4
    • 3gb7, 2p7t, 2h8p, 2hfe, 2atk, 4wfh, 4wfg, 4wff, 4wfe, 5vk6, 5vke, 5vkh, 6by2, 6by3 - mFab + KcsA K+ channel + ion
    • 3or6, 3or7, 3ogc, 3fb7, 3f7v, 3f7y, 3fb5, 3fb6, 3fb8, 3iga, 2itc, 2itd, 2nlj, 2bob, 2boc, 1s5h, 1r3i, 1r3j, 1r3k, 1r3l, 1k4c, 1k4d, 3hpl - mFab + KcsA K+ channel (mutant) + ion
    • 2fd6 – mFab ATN-615 + urokinase-type plasminogen activator + urokinase plasminogen receptor
    • 4k24 – mFab + urokinase-type plasminogen activator + urokinase plasminogen receptor + vitronectin
    • 1j5o – mFab + reverse transcriptase + DNA
    • 1qkz – mFab + protein G prime + major outer membrane protein peptide
    • 2ibz – mFab + cytochrome bc1 complex + stigmatellin
    • 6jmq, 6jmr – mFab + large neutral amino acid transporter + 4f2 cell-surface antigen
    • 6qno - mFab + guanine nucleotide-binding protein + transducin + rhodopsin – Cryo EM
    • 7k78 - mFab + yeast nucleosome – Cryo EM
    • 7rxc, 7rxd - mFab + viVVH + ER lumen receptors – Cryo EM
    • 7c6a – mFab + angiotensin receptor + SAR1
    • 6gff – mFab + TGF + GARPIN
    • 7kpb – mFab + TNF + TNFR
    • [[7df9], 7dfa, 7dfb, 7dfc] – mFab + arrestin + arrestin receptor
  • Full Immunoglobulin
    • 1hzh - hFab IgG B12
    • 1iga - hIgA1 - model
  • Fc Fragments or immunoglobulin gamma-1 heavy chain
  • Fv Fragments
    • 3zhd, 3zhk, 3zhl – hFv scaffold
    • 4u3x – hFv + lysozyme
    • 3dur, 3dus, 3duu, 3dv4, 3dv6 – mFv + Ig-like protein
    • 3hb3 – mFv + cytochrome c oxidase subunit 1-β
    • 1qle - mFv + cytochrome c oxidase
    • 6oik - mFv + AChR + guanine nucleotide-binding protein + transducin – Cryo EM
  • Single chain variable fragment (scFv)
  • Single chain variable fragment complex
    • 5lbs – hscFv + zika envelope protein E
    • 5ljy – hscFv + Hantaan virus envelope protein
    • 6pcu – hscFv + rotavirus capsid protein
    • 7cth – hscFv + dengue protein – Cryo EM
    • 4nik – hscFv + gankyrin
    • 5jz7 – hscFv + NGF
    • 4kv5 – hscFv + TGF
    • 6tou – hscFv + rabies glycoprotein
    • 6ikm – hscFv + polyamine transport protein
    • 2ybr, 2yc1 – hscFv + CN2 toxin
    • 5ujz, 5uk0, 5uk1, 5uk2 - hscFv + hemagglutinin – Cryo EM
    • 4v1d - hscFv + mammal toxin CN2
    • 6i07 – hscFv + EpCAM
    • 6kn9 – hscFv + IL-18R
    • 5d9q – hscFv + antibody + gp120 + gp40
    • 7jum – hscFv + P230
    • 7tzg, 7tzh – hscFv + LAG3
    • 7xw7 – hscFv + thyrotropin receptor – Cryo EM
    • 6e0c, 6e0p - hscFv in nucleosome – Cryo EM
    • 8dpf, 8dpg, 8dph, 8dpi – hscFv + Gi + 5HT2C receptor + drug – Cryo EM
    • 7jvr – hscFv + Gi + dopamine receptor + drug – Cryo EM
    • 7tuz – hscFv + Gi + GPR183 + drug – Cryo EM
    • 7d3k, 7d3l, 7d3m, 7d3r – bscFv + FMDV proteins – Cryo EM
    • 3ab0 – mscFv + BCLA protein
    • 5jyl, 5jym – mscFv + cadherin
    • 5f3j – mscFv + duffy receptor
    • 5dfw, 6ejg, 6ejm, 6ek2 – mscFv + CD81
    • 2kh2 – mscFv + IL-1 - NMR
    • 4yqx – mscFv + IL-2
    • 3h3b – mscFv + ERBB2
    • 5ogi – mscFv + hexon protein
    • 3h3b, 6eqc – mscFv + hexon protein – Cryo EM
    • 7rkf, 7rkm, 7rkn, 7rkx, 7rky – mscFv + Gi + US27 – Cryo EM
    • 7xmt – mscFv + Gi + SSTR4 – Cryo EM
    • 7jhj – mscFv + Gi + BILF1 – Cryo EM
    • 4f9p, 4f9l – mscFv + BTN3A1
    • 5aam, 5aaw, 7k93 – mscFv + Dengue virus envelope protein
    • 5kov – mscFv + Astrovirus envelope protein
    • 7rk1 – mscFv + Astrovirus VP70
    • 7rk2 – mscFv + Astrovirus VP25
    • 6h3t, 6h3u – mscFv + bovine schmallenberg virus envelope protein
    • 1dzb, 2znx – mscFv + lysozyme
    • 1a14, 1nmc – mscFv + neuraminidase
    • 1fo0, 1kj2, 1nam – mscFv + TCR + MHC + peptide
    • 7k5x, 7k5y, 7k60, 7k61, 7k63 - mscFv + human nucleosome – Cryo EM
    • 6lgw – rmscFv + rabies glycoprotein
  • Single chain variable fragment complex with small molecule
    • 5i4f, 5vf2 – mscFv + mannobiose
    • 4h0i – mscFv + mannopyranoside
    • 2cju – mscFv + phOxGABA
    • 2uud – mscFv + hapten
    • 5j74, 5j75 – hscFv + inhibitor
    • 4lar – hscFv + dexedrine
    • 4las – hscFv + amphetamine derivative
    • 6k4z – mscFv + NPA
  • Single chain variable fragment complex with peptide
  • Single domain antibody VHH or Camelid antibody or nanobody or single domain antibody or sybody
  • VHH binary complexes
  • VHH ternary complexes
    • 3v0a – LgVHH + BONT/A1 + NTNH
    • 3sn6 – LgVHH + adrenergic receptor + guanine nucleotide-binding protein
    • 7bts, 7bu6 – LgVHH + adrenergic receptor + epinephrine
    • 6oya - LgVHH + guanine nucleotide-binding protein + transducin + rhodopsin + GT-alpha/GI1-alpha – Cryo EM
    • 4laj - LgVHH + envelope glycoprotein gp120 + CD4
    • 4orz – LgVHH + tyrosine protein kinase HCK + NEF
    • 6v7z – LgVHH + CD1d + b-2-microglobulin
    • 6v80 – LgVHH + CD1d + NKT TCR + b-2-microglobulin
    • 4kro, 4krp – LgVHH + antibody + EGFR
    • 7q6c – LgVHH + complement C1 + antibody
    • 5j1s, 5j1t – ViVHH + Torsin + LULL1
    • 5uk4, 5ukb – ViVHH + virus capsid + RNA
    • 5jmo – cVHH + furin + CMK inhibitor
    • 5fuc – cVHH + IL-6 + IL-6R
    • 6h7j, 6h7l, 6h7m, 6h7o, 6ibl – cVHH + thioredoxin + adrenergic receptor
    • 6n48 – cVHH + modulator + adrenergic receptor
    • 6do1 – syVHH + BRIL + S1I8 peptide
  • Intrabody or anti-helix antibody
    • 6k67 – hIB 3LRH + calmodulin
    • 6k3m, 6k64, 6k6a, 6k6b – hIB 3LRH + SpA IgG-binding domain protein
    • 6k69 – hIB 3LRH + T4 lysozyme
  • Diabody or single chain Fv

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