SMTL ID : 3woi.2 (1 other biounit)

Crystal structure of the DAP BII (S657A)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: R.389, Y.405, M.508, L.511, E.515, R.518 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.389, A:R.389, A:Y.405, A:E.515, A:R.518 Water bridges: A:E.515, A:E.515, A:R.518, A:R.518 GOL.2: 3 residues within 4Å: Chain A: D.188, N.305, K.309 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.305, A:K.309 Water bridges: A:N.305, A:N.305, A:K.309 GOL.3: 7 residues within 4Å: Chain A: Y.65, K.184, D.188, A.298, M.301, A.302, N.305 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.65, A:K.184, A:D.188, A:A.298, A:N.305 Water bridges: A:N.306 GOL.4: 7 residues within 4Å: Chain A: D.569, G.570, M.571 Chain B: T.574, F.576, T.578, I.615 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.569, A:G.570, B:T.574, B:I.615 GOL.5: 8 residues within 4Å: Chain A: W.192, I.628, T.629, G.630, A.633, F.649, D.650, G.651 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.649 Water bridges: A:H.62, A:A.633, A:D.650, A:S.655 GOL.9: 6 residues within 4Å: Chain B: R.389, Y.405, M.508, L.511, E.515, R.518 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.389, B:R.389, B:R.518 Water bridges: B:Y.405, B:E.515, B:E.515, B:R.518, B:R.518 GOL.10: 3 residues within 4Å: Chain B: D.188, N.305, K.309 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.305, B:K.309 Water bridges: B:D.188, B:N.305, B:N.305, B:K.309 GOL.11: 7 residues within 4Å: Chain B: Y.65, K.184, D.188, A.298, M.301, A.302, N.305 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.65, B:K.184, B:D.188, B:A.298, B:N.305 Water bridges: B:Y.65, B:N.306 GOL.12: 7 residues within 4Å: Chain A: T.574, F.576, T.578, I.615 Chain B: D.569, G.570, M.571 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.569, B:G.570, A:I.615 GOL.13: 8 residues within 4Å: Chain B: W.192, I.628, T.629, G.630, A.633, F.649, D.650, G.651 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:F.649 Water bridges: B:H.62, B:A.633, B:D.650, B:S.655

6 x ZN: ZINC ION(Non-covalent)

ZN.6: 3 residues within 4Å: Chain A: D.35, K.227, H.228 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.35, A:D.35, A:H.228, H2O.23 ZN.7: 1 residues within 4Å: Chain A: D.123 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.123, A:D.123, H2O.23, H2O.27 ZN.8: 4 residues within 4Å: Chain A: N.191, W.192, N.306, D.650 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.650, H2O.14 ZN.14: 3 residues within 4Å: Chain B: D.35, K.227, H.228 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.35, B:D.35, B:H.228, H2O.49 ZN.15: 1 residues within 4Å: Chain B: D.123 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.123, B:D.123, H2O.49, H2O.53 ZN.16: 4 residues within 4Å: Chain B: N.191, W.192, N.306, D.650 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.650, H2O.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sakamoto, Y. et al., S46 peptidases are the first exopeptidases to be members of clan PA. SCI REP (2014)

Release Date

2014-09-03

Peptides

dipeptidyl aminopeptidase BII: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

dipeptidyl aminopeptidase BII

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