SMTL ID : 4y06.2 (1 other biounit)

Crystal structure of the DAP BII (G675R) dipeptide complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

monomer

Ligands

1 x LEU: LEUCINE(Non-covalent)

LEU.1: 9 residues within 4Å: Chain A: H.86, N.215, W.216, R.220, D.224, N.330, F.673, D.674 Ligands: GLU.2 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:H.86 Hydrogen bonds: A:N.215, A:N.215, A:N.330

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.2: 12 residues within 4Å: Chain A: H.86, W.216, I.652, T.653, G.654, G.655, N.656, S.657, F.673, D.674, R.675 Ligands: LEU.1 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:I.652 Hydrogen bonds: A:T.653, A:G.655, A:N.656, A:S.657, A:S.657, A:F.673 Water bridges: A:G.654, A:G.654 Salt bridges: A:H.86, A:R.675

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: M.404, Y.448, A.450, D.453, R.454, Q.457, L.495, A.496, T.498 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.448, A:Q.457 Water bridges: A:R.454, A:R.454 GOL.4: 7 residues within 4Å: Chain A: M.217, W.218, Y.589, Y.597, N.676, W.677, E.678 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.218, A:Y.589, A:Y.597, A:W.677, A:E.678 GOL.5: 7 residues within 4Å: Chain A: G.90, A.91, L.94, A.118, A.122, Q.443, R.447 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.90, A:Q.443, A:R.447, A:R.447 Water bridges: A:C.87, A:G.90, A:A.91 GOL.6: 5 residues within 4Å: Chain A: G.406, S.407, Q.410, G.440, L.441 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.440 GOL.7: 3 residues within 4Å: Chain A: D.214, P.219, K.609 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.609 Water bridges: A:W.218 GOL.8: 3 residues within 4Å: Chain A: D.258, Q.259, H.665 No protein-ligand interaction detected (PLIP) GOL.9: 2 residues within 4Å: Chain A: D.593, G.594 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.593, A:G.594, A:M.595 GOL.10: 6 residues within 4Å: Chain A: A.257, D.258, Q.259, P.260, R.699, R.702 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.634, A:R.702 Water bridges: A:Q.259, A:R.699

2 x ZN: ZINC ION(Non-covalent)

ZN.11: 1 residues within 4Å: Chain A: E.438 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.438, A:E.438 ZN.12: 1 residues within 4Å: Chain A: E.635 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.635, A:E.635, H2O.1, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sakamoto, Y. et al., Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity. Sci Rep (2015)

Release Date

2015-07-15

Peptides

Dipeptidyl aminopeptidase BII: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Dipeptidyl aminopeptidase BII

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