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Open data
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Basic information
Entry | Database: PDB / ID: 4d2d | ||||||
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Title | Structure of a tri peptide bound POT family peptide transporter | ||||||
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![]() | TRANSPORT PROTEIN / MAJOR FACILITATOR SUPERFAMILY / PROTON OLIGOPEPTIDE TRANSPORTER (POT) FAMILY / PEPTIDE TRANSPORTER / TRIPEPTIDE COMPLEX | ||||||
Function / homology | ![]() oligopeptide transport / peptide transmembrane transporter activity / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() SYNTHETIC CONSTRUCT (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lyons, J.A. / Parker, J.L. / Solcan, N. / Brinth, A. / Li, D. / Shah, S.T.A. / Caffrey, M. / Newstead, S. | ||||||
![]() | ![]() Title: Structural Basis for Polyspecificity in the Pot Family of Proton-Coupled Oligopeptide Transporters. Authors: Lyons, J.A. / Parker, J.L. / Solcan, N. / Brinth, A. / Li, D. / Shah, S.T. / Caffrey, M. / Newstead, S. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.7 KB | Display | ![]() |
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PDB format | ![]() | 81.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 19.4 KB | Display | |
Data in CIF | ![]() | 26.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d2bC ![]() 4d2cC ![]() 4apsS C: citing same article ( S: Starting model for refinement |
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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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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 53721.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 231.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
-Non-polymers , 4 types, 52 molecules ![](data/chem/img/78M.gif)
![](data/chem/img/78N.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/78N.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.3 % / Description: NONE |
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Crystal grow | Method: lipidic cubic phase / pH: 7 Details: 16-23 %(V/V) PEG 400, 0.1 M HEPES PH 7.0, 0.15-0.55 M NH4H2PO4 AND 10 MM TRI-ALANINE. CRYSTALS WERE GROWN BY THE LCP METHOD WITH 7.8 MAG AS HOSTING LIPID. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 2, 2012 / Details: K-B PAIR OF BIOMORPH MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→75.56 Å / Num. obs: 21341 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 44.26 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.52→2.59 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.2 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4APS Resolution: 2.522→75.556 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 24.67 / Stereochemistry target values: ML Details: RESIDUES 1-5, 272-275, 414-419, 479-491 ARE DISORDERED TRIPEPTIDE WAS MODELED WITH ITS C-TERMINUS ORIENTATED TOWARDS THE EXTRACELLULAR SIDE. SEE PAPER FOR FURTHER DISCUSSION.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.229 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.522→75.556 Å
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Refine LS restraints |
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LS refinement shell |
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