Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution (rhombohedral form)
Joint Center for Structural Genomics (JCSG)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 |
Putative phosphomethylpyrimidine kinase | 291 | Bacteroides thetaiotaomicron VPI-5482 | Mutation(s): 0  Gene Names: BT_4458 | ||
UniProt | |||||
Find proteins for Q89ZB9 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q89ZB9  Go to UniProtKB:  Q89ZB9 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q89ZB9 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 6 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
MRD Query on MRD | J [auth A], L [auth A] | (4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N | |||
MPD Query on MPD | I [auth A], K [auth A] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N | |||
SO4 Query on SO4 | F [auth A], G [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
IMD Query on IMD | H [auth A] | IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O | |||
ZN Query on ZN | B [auth A], C [auth A], D [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
CL Query on CL | E [auth A] | 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 | L-PEPTIDE LINKING | C5 H11 N O2 Se | MET |
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 161.627 | α = 90 |
b = 161.627 | β = 90 |
c = 76.138 | γ = 120 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
PHENIX | refinement |
SHELX | phasing |
MolProbity | model building |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
autoSHARP | phasing |
SHELXD | phasing |