SMTL ID : 3wor.1

Crystal structure of the DAP BII octapeptide complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x ASP- ARG- VAL- TYR- ILE- HIS: Angiotensin II(Non-covalent)

ASP-ARG-VAL-TYR-ILE-HIS.1: 21 residues within 4Å: Chain A: G.45, C.46, N.191, W.192, R.196, G.250, Y.276, N.306, T.307, N.310, Y.311, I.628, T.629, G.630, G.631, N.632, A.633, F.649, D.650, G.651, S.655 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.628 Hydrogen bonds: A:G.45, A:N.191, A:N.191, A:Y.276, A:N.306, A:G.631, A:A.633, A:F.649, A:F.649, A:S.655 Water bridges: A:N.60, A:R.196, A:R.196, A:N.310, A:N.310, A:G.630, A:G.630, A:S.655 Salt bridges: A:R.196 ASP-ARG-VAL-TYR-ILE-HIS.2: 21 residues within 4Å: Chain B: G.45, C.46, N.191, W.192, R.196, G.250, Y.276, N.306, T.307, Y.311, L.553, I.628, T.629, G.630, G.631, N.632, A.633, F.649, D.650, G.651, S.655 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:T.307, B:L.553, B:I.628, B:A.633 Hydrogen bonds: B:G.45, B:N.191, B:N.191, B:Y.276, B:N.306, B:T.629, B:T.629, B:G.631, B:N.632, B:A.633, B:F.649, B:D.650, B:S.655 Water bridges: B:N.60, B:K.184, B:R.196, B:R.196, B:G.250, B:G.630, B:G.630, B:S.655 Salt bridges: B:R.196

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: T.574, F.576, I.615 Chain B: D.569, G.570 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.569, B:G.570, B:M.571, A:I.615 GOL.4: 5 residues within 4Å: Chain A: D.35, K.227, H.228, W.229, K.231 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.228, A:W.229, A:W.229 GOL.5: 7 residues within 4Å: Chain A: A.42, G.44, F.101, R.149, R.151, Y.153, N.166 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.151, A:R.151, A:N.166 Water bridges: A:G.45 GOL.6: 8 residues within 4Å: Chain A: Y.65, K.184, D.188, A.298, M.301, A.302, N.305 Ligands: GOL.8 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.65, A:K.184, A:M.301, A:N.305 Water bridges: A:D.188, A:D.188, A:Q.294, A:Q.294 GOL.7: 6 residues within 4Å: Chain A: C.63, A.64, G.66, A.67, A.98, Y.204 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:C.63, A:G.66, A:A.67, A:N.97 Water bridges: A:Y.65, A:Y.204, A:Q.419, A:Q.419, A:R.423 GOL.8: 5 residues within 4Å: Chain A: N.77, K.80, Q.294, V.295 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.77, A:N.77, A:Q.294, A:Q.294 GOL.9: 6 residues within 4Å: Chain A: R.389, Y.405, M.508, L.511, E.515, R.518 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.389, A:E.515, A:R.518 Water bridges: A:N.376, A:L.511, A:R.518 GOL.12: 5 residues within 4Å: Chain A: D.569, G.570 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, B:T.574, B:I.615 Water bridges: A:M.571 GOL.13: 5 residues within 4Å: Chain B: T.33, V.102, L.103, D.104, L.167 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.224

4 x ZN: ZINC ION(Non-covalent)

ZN.10: 2 residues within 4Å: Chain A: E.481, K.484 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.481, A:E.481, H2O.23 ZN.11: 2 residues within 4Å: Chain A: K.23, H.641 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.641, H2O.23 ZN.14: 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.36 ZN.15: 2 residues within 4Å: Chain B: K.23, H.641 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.641, H2O.39

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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