SMTL ID : 3wom.1

Crystal structure of the DAP BII dipeptide complex II

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

2 x VAL: VALINE(Non-covalent)

VAL.1: 8 residues within 4Å: Chain A: H.62, N.191, W.192, R.196, N.306, F.649, D.650 Ligands: TYR.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:N.191, A:N.306, A:D.650, Y.2 VAL.11: 9 residues within 4Å: Chain B: H.62, N.191, W.192, R.196, D.200, N.306, F.649, D.650 Ligands: TYR.12 4 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain B Hydrogen bonds: Y.12, B:N.191, B:N.191, B:N.306

2 x TYR: TYROSINE(Non-covalent)

TYR.2: 13 residues within 4Å: Chain A: H.62, W.192, I.628, T.629, G.630, G.631, N.632, S.633, F.649, D.650, G.651, S.655 Ligands: VAL.1 12 PLIP interactions: 11 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.192, A:W.192, A:I.628 Hydrogen bonds: A:G.631, A:S.633, A:S.633, A:F.649, A:S.655, V.1 Water bridges: A:I.628, A:V.656 Salt bridges: A:H.62 TYR.12: 13 residues within 4Å: Chain B: H.62, W.192, I.628, T.629, G.630, G.631, N.632, S.633, F.649, D.650, G.651, S.655 Ligands: VAL.11 12 PLIP interactions: 11 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:W.192, B:W.192, B:I.628 Hydrogen bonds: B:G.631, B:S.633, B:S.633, B:F.649, B:S.655, V.11 Water bridges: B:I.628, B:V.656 Salt bridges: B:H.62

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: T.574, F.576, I.615 Chain B: D.569, G.570, M.571 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:I.615, B:D.569, B:G.570, B:M.571 Water bridges: A:T.574, B:E.572 GOL.4: 5 residues within 4Å: Chain A: D.35, K.227, H.228, W.229, K.231 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.228, A:H.228, A:W.229, A:W.229, A:K.231 GOL.5: 5 residues within 4Å: Chain A: G.44, F.101, R.149, R.151, N.166 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.151 Water bridges: A:G.44, A:R.149 GOL.6: 5 residues within 4Å: Chain A: R.389, M.508, L.511, E.515, R.518 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.389, A:E.515, A:R.518 Water bridges: A:N.376, A:R.518 GOL.7: 5 residues within 4Å: Chain A: N.77, I.79, Q.294, V.295, A.298 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.77 GOL.8: 7 residues within 4Å: Chain A: A.233, D.234, Q.235, P.236, G.609, L.610, R.675 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.609 Water bridges: A:Q.235, A:R.675, A:R.675, A:R.678, A:R.678 GOL.13: 6 residues within 4Å: Chain A: D.569, G.570, M.571 Chain B: T.574, F.576, I.615 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.569, A:G.570, A:M.571, B:T.574, B:I.615 GOL.14: 5 residues within 4Å: Chain B: D.35, K.227, H.228, W.229, K.231 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.228, B:W.229, B:W.229 GOL.15: 5 residues within 4Å: Chain B: G.44, F.101, R.149, R.151, N.166 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.149, B:R.151 Water bridges: B:G.45, B:Y.153 GOL.16: 6 residues within 4Å: Chain B: A.233, D.234, Q.235, L.610, R.675, R.678 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.234, B:G.609, B:R.675 Water bridges: B:R.678

4 x ZN: ZINC ION(Non-covalent)

ZN.9: 1 residues within 4Å: Chain A: H.641 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.641, H2O.21 ZN.10: 2 residues within 4Å: Chain A: E.481, K.484 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.481, H2O.21 ZN.17: 2 residues within 4Å: Chain B: K.23, H.641 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.641 ZN.18: 2 residues within 4Å: Chain B: E.481, K.484 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.481, B:E.481, H2O.38

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
B

dipeptidyl aminopeptidase BII

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