SMTL ID : 3woi.1 (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

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: A.233, D.234, Q.235, P.236, L.610, R.675, R.678 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.234, A:G.609 Water bridges: A:A.233, A:R.675 GOL.2: 6 residues within 4Å: Chain A: T.574, F.576, I.615 Chain B: D.569, G.570, M.571 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.574, A:I.615, B:D.569, B:G.570 GOL.6: 7 residues within 4Å: Chain B: A.233, D.234, Q.235, P.236, L.610, R.675, R.678 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.234, B:G.609 Water bridges: B:A.233, B:R.675, B:R.678 GOL.7: 6 residues within 4Å: Chain A: D.569, G.570, M.571 Chain B: T.574, F.576, I.615 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:I.615, A:D.569, A:G.570 Water bridges: B:T.574

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 1 residues within 4Å: Chain A: H.641 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.641, H2O.11, H2O.12 ZN.4: 3 residues within 4Å: Chain A: D.35, K.227, H.228 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.35, A:H.228, H2O.12 ZN.5: 1 residues within 4Å: Chain A: E.611 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.611, A:E.611, H2O.13 ZN.8: 1 residues within 4Å: Chain B: H.641 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.641, H2O.24, H2O.24 ZN.9: 3 residues within 4Å: Chain B: D.35, K.227, H.228 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.35, B:H.228, H2O.25 ZN.10: 1 residues within 4Å: Chain B: E.611 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.611, B:E.611, H2O.25

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
A

B
A

dipeptidyl aminopeptidase BII

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