Crystal Structure of Periplasmic Dipeptide Transport Protein from Yersinia pestis
Kim, Y., Zhou, M., Shatsman, S., Anderson, W.F., Joachimiak, A.To be published.
Experimental Data Snapshot
wwPDB Validation   3D Report Full Report
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Periplasmic dipeptide transport protein | 543 | Yersinia pestis Nepal516 | Mutation(s): 0  Gene Names: YPN_3652 | ||
UniProt | |||||
Find proteins for A0A0H2YM47 (Yersinia pestis bv. Antiqua (strain Nepal516)) Explore A0A0H2YM47  Go to UniProtKB:  A0A0H2YM47 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A0A0H2YM47 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 5 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
GLN Query on GLN | J [auth A], K [auth A], R [auth B], S [auth B] | GLUTAMINE C5 H10 N2 O3 ZDXPYRJPNDTMRX-VKHMYHEASA-N | |||
PEG Query on PEG | F [auth A] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N | |||
GOL Query on GOL | D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
EDO Query on EDO | C [auth A] E [auth A] G [auth A] I [auth A] L [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N | |||
CL Query on CL | H [auth A], O [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Modified Residues 1 Unique | |||||
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ID | Chains | Type | Formula | 2D Diagram | Parent |
MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se | MET |
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 289.29 | α = 90 |
b = 59.745 | β = 103.96 |
c = 80.631 | γ = 90 |
Software Name | Purpose |
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PHENIX | refinement |
HKL-3000 | data scaling |
HKL-3000 | phasing |
SBC-Collect | data collection |
Funding Organization | Location | Grant Number |
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National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | -- |