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- PDB-1nmc: COMPLEX BETWEEN NC10 ANTI-INFLUENZA VIRUS NEURAMINIDASE SINGLE CH... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nmc | |||||||||
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Title | COMPLEX BETWEEN NC10 ANTI-INFLUENZA VIRUS NEURAMINIDASE SINGLE CHAIN ANTIBODY WITH A 15 RESIDUE LINKER AND INFLUENZA VIRUS NEURAMINIDASE | |||||||||
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![]() | COMPLEX (SINGLE-CHAIN ANTIBODY/ANTIGEN) / COMPLEX (SINGLE-CHAIN ANTIBODY-ANTIGEN) / HYDROLASE / COMPLEX (SINGLE-CHAIN ANTIBODY-ANTIGEN) complex | |||||||||
Function / homology | ![]() exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Malby, R.L. / Mccoy, A.J. / Kortt, A.A. / Hudson, P.J. / Colman, P.M. | |||||||||
![]() | ![]() Title: Three-dimensional structures of single-chain Fv-neuraminidase complexes. Authors: Malby, R.L. / McCoy, A.J. / Kortt, A.A. / Hudson, P.J. / Colman, P.M. #1: ![]() Title: Recombinant Antineuraminidase Single Chain Antibody: Expression, Characterization, and Crystallization in Complex with Antigen Authors: Malby, R.L. / Caldwell, J.B. / Gruen, L.C. / Harley, V.R. / Ivancic, N. / Kortt, A.A. / Lilley, G.G. / Power, B.E. / Webster, R.G. / Colman, P.M. / Hudson, P.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 256.1 KB | Display | ![]() |
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PDB format | ![]() | 210.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 48.4 KB | Display | |
Data in CIF | ![]() | 66.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1a14C ![]() 1ncaS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.998491, 0.05492, -0.000553), Vector: |
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Components
-Protein , 1 types, 2 molecules NA
#1: Protein | Mass: 43723.770 Da / Num. of mol.: 2 / Fragment: RESIDUES 82 - 468 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Antibody , 2 types, 4 molecules HBLC
#2: Antibody | Mass: 13399.659 Da / Num. of mol.: 2 Fragment: VH AND VL DOMAINS OF ANTI-NEURAMINIDASE ANTIBODY NC10 COVALENTLY JOINED BY A FIFTEEN RESIDUE POLYPEPTIDE LINKER Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Antibody | Mass: 12162.203 Da / Num. of mol.: 2 Fragment: VH AND VL DOMAINS OF ANTI-NEURAMINIDASE ANTIBODY NC10 COVALENTLY JOINED BY A FIFTEEN RESIDUE POLYPEPTIDE LINKER Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 3 types, 8 molecules ![](data/chem/img/MAN.gif)
![](data/chem/img/NAG.gif)
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#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | #6: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 182 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | THE THREE OLIGOSACCHARIDES COVALENTLY ATTACHED TO N9 NEURAMINIDASE ARE NUMBERED BY THE ASN RESIDUE ...THE THREE OLIGOSACCH |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 70 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6.6 Details: NC10 SCFV(15) AND N9 NA WERE MIXED TOGETHER (SCFV(15) IN SLIGHT MOLAR EXCESS) WITH AND EQUAL VOLUME OF POTASSIUM PHOSPHATE BUFFER 1.7M PH6.6. THE DROP WAS EQUILIBRATED BY VAPOUR DIFFUSION ...Details: NC10 SCFV(15) AND N9 NA WERE MIXED TOGETHER (SCFV(15) IN SLIGHT MOLAR EXCESS) WITH AND EQUAL VOLUME OF POTASSIUM PHOSPHATE BUFFER 1.7M PH6.6. THE DROP WAS EQUILIBRATED BY VAPOUR DIFFUSION AGAINST PHOSPHATE BUFFER 1.3M PH6.8. PH range: 6.6-6.8 | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: Malby, R.L., (1993) Proteins: Struct.,Funct., Genet., 16, 57. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ![]() ![]() |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.5 Å / Num. obs: 67425 / % possible obs: 80 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.104 |
Reflection shell | Resolution: 2.5→2.6 Å / % possible all: 70 |
Reflection | *PLUS Num. measured all: 156708 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1NCA Resolution: 2.5→7 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: A POSTERIORI / σ(F): 2
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Displacement parameters | Biso mean: 23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→7 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: STRICT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.65 Å / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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