4Y06: DAP BII (G675R) dipeptide complex

Crystal structure of the DAP BII (G675R) dipeptide complex. Determined by X-ray diffraction at 2.18 Å resolution. Released 15 Jul 2015.

Method

X-ray diffraction

Resolution

2.18 Å

Organism

Pseudoxanthomonas mexicana

Chains

2

Atoms

11,405

Mol. weight

159.95 kDa

Ligands

ZN, GLU, LEU

Released

15 Jul 2015

Explore 4Y06 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Y06 contains 87 α-helices and 50 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 43 helices, 24 β-strands

Molecules and chains

>4Y06_1 Dipeptidyl aminopeptidase BII (chains A, B)
MRPNLLAAAIAVPLSLLAAQIAQAGEGMWVPQQLPEIAGPLKKAGLKLSPQQISDLTGDP
MGAVVALGGCTASFVSPNGLVVTNHHCAYGAIQLNSTAENNLIKNGFNAPTTADEVSAGP
NARVFVLDEITDVTKDAKAAIAAAGDDALARTKALEAFEKKLIADCEAEAGFRCRLYSFS
GGNTYRLFKNLEIKDVRLAYAPPGSVGKFGGDIDNWMWPRHTGDFAFYRAYVGKDGKPAA
FSKDNVPYQPKHWLKFADQPLGAGDFVMVAGYPGSTNRYALAAEFDNTAQWTYPTIARHY
KNQIAMVEAAGKQNADIQVKYAATMAGWNNTSKNYDGQLEGFKRIDAAGQKLREEAAVLG
WLKGQGAKGQPALDAHAKLLDLLEQSKATRDRDLTLALFNNTAMLGSATQLYRLSIEREK
PNAERESGYQERDLPAIEGGLKQLERRYVAAMDRQLQEYWLNEYIKLPADQRVAAVDAWL
GGNDAAAVKRALDRLAGTKLGSTEERLKWFAADRKAFEASNDPAIQYAVAVMPTLLKLEQ
ERKTRAGENLAARPVYLQALADYKKSQGEFVYPDANLSLRITFGNVMGYAPKDGMEYTPF
TTLEGVVAKETGQDPFDSPKALLDAVAAKRYGGLEDKRIGSVPVNYLSDLDITGGNSGSP
VLDAHGKLVGLAFDRNWESVSSNWVFDPKMTRMIAVDGRYLRWIMQEVYPAPQLLKEMNV
GK

Ligands and cofactors

Water and common crystallization additives (GOL) are not listed.

Primary citation

Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity. Sakamoto, Y., Suzuki, Y., Iizuka, I. et al. Sci Rep (2015) 5:11151-11151. DOI 10.1038/srep11151 · PubMed

Related structures

Other PDB entries of the same protein (UniProt V5YM14 (AlphaFold model), which also has an AlphaFold model), best resolution first:

• 3WOL 1.74 Å, Crystal structure of the DAP BII dipeptide complex I
• 3WON 1.75 Å, Crystal structure of the DAP BII dipeptide complex III
• 3WOO 1.8 Å, Crystal structure of the DAP BII hexapeptide complex I
• 3WOQ 1.82 Å, Crystal structure of the DAP BII hexapeptide complex III
• 3WOM 1.86 Å, Crystal structure of the DAP BII dipeptide complex II
• 3WOK 1.95 Å, Crystal structure of the DAP BII (Space)
• 3WOP 1.95 Å, Crystal structure of the DAP BII hexapeptide complex II
• 3WOI 2.1 Å, Crystal structure of the DAP BII (S657A)
• 3WOR 2.1 Å, Crystal structure of the DAP BII octapeptide complex
• 3WOJ 2.2 Å, Crystal structure of the DAP BII

Browse structure collections

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