Crystal structure of a Putative gamma-D-glutamyl-L-diamino acid endopeptidase (DVU_0896) from DESULFOVIBRIO VULGARIS HILDENBOROUGH at 1.75 A resolution
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 gamma-D-glutamyl-L-diamino acid endopeptidase | 434 | Nitratidesulfovibrio vulgaris str. Hildenborough | Mutation(s): 0  Gene Names: DVU_0896 | ||
UniProt | |||||
Find proteins for Q72DN3 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72DN3  Go to UniProtKB:  Q72DN3 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q72DN3 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 4 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
MES Query on MES | I [auth A], U [auth B] | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N | |||
GOL Query on GOL | C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
ACT Query on ACT | H [auth A], T [auth B] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M | |||
CL Query on CL | J [auth A] K [auth A] L [auth A] M [auth A] V [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 ( ˚ ) |
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a = 59.337 | α = 90 |
b = 54.465 | β = 94.06 |
c = 122.982 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
PHENIX | refinement |
SHELX | phasing |
MolProbity | model building |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
SHELXD | phasing |
autoSHARP | phasing |