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EBI Services Structure Databases ProFunc Results

ProFunc results for 1aif

 

 

 

 

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JSmol   RasMol
ProFunc id: 1aif
 
Header details

Structure: 		ANTI-IDIOTYPIC FAB 409.5.3 (IGG2A) FAB FROM MOUSE

Source: 		Ms musculus. Houemouse. Oorganis_axiidd: 10090. Ms musculus.. Hos mouse. Oorganim_taxiid 110900

Date: 		14 Nov 94

Author(s): 		N.Ban,C.Escobar,K.Hasel,J.Day,A.Greenwood,A.Mcpherson

Resolution: 		2.000Å      

Summary of predicted function

+ Protein name terms
fab (259.41) region (246.98) heavy (191.96) os=homo (191.07) antibody (184.07) os=homo sapiens (183.91) os=mus (163.68) os=mus musculus (149.57)

+ Gene Ontology (GO) terms
Cellular component: extracellular region (18.27) extracellular region part (18.27) extracellular space (18.27) macromolecular complex (18.10)
Biological process: immune system process (18.27) immune response (18.27) response to stimulus (18.27) adaptive immune response (18.10)
Biochemical function: binding (18.26) antigen binding (17.34) immunoglobulin receptor binding (17.34) protein binding (17.34)
The protein names and GO terms above are the most common terms found in the hits obtained from the analyses below. Each term's score (based on the number of times it occurs independently) is given in brackets. Click on the plus icons for a complete breakdown of which programs, and further, which hits the terms came from.

ProFunc results

Sequence motifs

InterPro scan for sequence motifs. Chains L, A

 

InterPro scan for sequence motifs. Chains H, B

13 motifs matched in scan against PROSITE, PRINTS, PFam-A, TIGRFAM, PROFILES and PRODOM motifs

  Type Motif Name
1. FunFam G3DSA:2.60.40.10x2 Immunoglobulins
2. ProSiteProfiles PS50835x2 Ig-like domain profile.
3. FunFam G3DSA:2.60.40.10:FF:0Ig  Ig gamma-2A chain C region
4. SUPERFAMILY SSF48726x2 Immunoglobulin
5. Pfam PF07686 Immunoglobulin V-set domain
... plus others

Matches to existing PDB structures

Sequence search vs existing PDB entries. Chains L, A

399 matching sequences found by FASTA search

  PDB code E-value %-tage id Overlap Name
1. 1iai(M) 2e-41 100.000 215 Idiotype-anti-idiotype fab complex
2. 5d8j(L) 5.6e-39 95.327 214 Development of a therapeutic monoclonal antibody targeting secreted ap2 to treat type 2 diabetes.
3. 6n4q(I) 6.5e-39 95.349 215 Cryoem structure of nav1.7 vsd2 (actived state) in complex with the gating modifier toxin protx2
4. 6n4r(I) 6.5e-39 95.349 215 Cryoem structure of nav1.7 vsd2 (deactived state) in complex with the gating modifier toxin protx2
5. 8vgl(L) 6.5e-39 95.349 215 Cryoem structure of nav1.7 in complex with wild type fab 7a9
... plus others
Sequence search vs existing PDB entries. Chains H, B

399 matching sequences found by FASTA search

  PDB code E-value %-tage id Overlap Name
1. 1iai(I) 7.2e-55 100.000 218 Idiotype-anti-idiotype fab complex
2. 1sbs(H) 7.2e-48 88.688 221 Crystal structure of an anti-hcg fab
3. 5x0t(A) 2.5e-46 87.615 218 Crystal structure of cd147 c2 domain in complex with fab of its monoclonal antibody 6h8
4. 5x4g(A) 2.5e-46 87.615 218 Crystal structure of fab fragment of anti-cd147 monoclonal antibody 6h8
5. 8vev(A) 7.4e-45 85.388 219 Structure of a mouse igg antibody antigen-binding fragment (fab) targeting n6-methyladenosine (m6a), an RNA modification, m6a nucleoside ligand
... plus others

Sequence search

BLAST search vs Uniprot. Chains L, A

310 matching sequences found by BLAST search

  Ref. no. E-value %-tage id Overlap Name
1. P01837 3e-68 100.000 107 Immunoglobulin kappa constant OS=Mus musculus
2. P01836 6e-56 83.962 106 Ig kappa chain C region, A allele OS=Rattus norvegicus
3. P01835 7e-54 80.189 106 Ig kappa chain C region, B allele OS=Rattus norvegicus
4. P04940 1e-49 77.778 108 Ig kappa chain V-VI region NQ2-17.4.1 OS=Mus musculus
5. P01678 4e-49 79.817 109 Ig kappa chain V-VI region SAPC 10 OS=Mus musculus
... plus others
BLAST search vs Uniprot. Chains H, B

306 matching sequences found by BLAST search

  Ref. no. E-value %-tage id Overlap Name
1. P84751 9e-96 69.725 218 Ig heavy chain Mem5 (Fragment) OS=Mus musculus
2. P01801 6e-60 80.165 121 Ig heavy chain V-III region J606 OS=Mus musculus
3. P0DOX2 1e-59 52.074 217 Immunoglobulin alpha-2 heavy chain OS=Homo sapiens
4. P01796 5e-59 80.672 119 Ig heavy chain V-III region A4 OS=Mus musculus
5. P01802 2e-58 78.512 121 Ig heavy chain V-III region W3082 OS=Mus musculus
... plus others

Residue conservation analysis

Conservation mapped onto 3D structure.

 

Nest analysis

Nest analysis. Chains L, A

1 nest located in the structure

  Score No.
resid.		 Ave.
access-
ibility		 Cleft Ave.
conser-
vation		 Residues
1. 1.488 3 0.00 10 0.488 Asp171(L), Ser172(L), Thr173(L)
Nest analysis. Chains H, B

2 nests located in the structure

  Score No.
resid.		 Ave.
access-
ibility		 Cleft Ave.
conser-
vation		 Residues
1. 0.670 3 0.00 - 0.670 Gly165(H), Ser166(H), Leu167(H)
2. 0.603 3 0.00 - 0.603 Lys78(H), Ser79(H), Arg80(H)

Cleft analysis

Surface clefts.

 

3D functional template searches

Enzyme active site templates.

No hits obtained from any of the 3518 enzyme active site templates.

Ligand-binding templates.

20 significant hits out of 433012 ligand-binding templates.

  Score Template PDB Name
1. 816.000 GOLc0773 1rul Crystal structure (d) of u.V.-Irradiated cationic cyclization antibody 4c6 fab at ph 5.6 with a data set collected at ssrl beamline 11-1.
Het Group GOL
2. 766.312 GOLc0526 1ncw Cationic cyclization antibody 4c6 in complex with benzoic acid
Het Group GOL
3. 756.000 GOLc0770 1rua Crystal structure (b) of u.V.-Irradiated cationic cyclization antibody 4c6 fab at ph 4.6 with a data set collected at ssrl beamline 11-1.
Het Group GOL
4. 735.000 PGEc1144 6igu Crystal structure of the hydrolytic antibody fab 9c10
Het Group PGE
5. 716.000 GOLc0777 1rup Crystal structure (g) of native cationic cyclization antibody 4c6 fab at ph 8.5 with a data set collected at aps beamline 19-id
Het Group GOL
... plus others

DNA-binding templates.

3 significant hits out of 43256 DNA-binding templates.

  Score Template PDB Name
1. 419.812 c08891 3ivk Crystal structure of the catalytic core of an RNA polymerase ribozyme complexed with an antigen binding antibody fragment
DNA-binding template (7 of 8 from 3ivk)
2. 209.375 c06630 2r8s High resolution structure of a specific synthetic fab bound to p4-p6 RNA ribozyme domain
DNA-binding template (9 of 9 from 2r8s)
3. 200.000 c31767 6mwn Crystal structure of hepatitis a virus ires domain v in complex with fab havx
DNA-binding template (12 of 13 from 6mwn)

Reverse template comparison vs structures in PDB.

20 significant hits out of 800 auto-generated templates.

  Score Template PDB Name
1. 820.000 TMP00173 4zso Crystal structure of a complex between b7-h6, a tumor cell ligand for natural cytotoxicity receptor nkp30, and an inhibitory antibody
2. 820.000 TMP00173 5l7x Afamin antibody fragment, n14 fab, l1- glycosylated, crystal form ii
3. 820.000 TMP00173 2z92 Crystal structure of the fab fragment of anti-ciguatoxin antibody 10c9 in complex with ctx3c_abcde
4. 820.000 TMP00173 6lkt Crystal structure of the fab fragment of murine monoclonal antibody kh-1 against human herpesvirus 6b
5. 863.188 TMP00005 2bmk Fab fragment of plp-dependent catalytic antibody 15a9 in complex with phosphopyridoxyl-d-alanine
... plus others

Key

In the summaries above, the hits are coloured according to their likelihood of being correct as follows: certain matches, probable matches, possible matches, and long shots. If the reliability of a hit is unknown, it is shown in navy blue.

Generated on Thu 27 Nov 2025 spacer
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