SMTL ID : 3woo.1

Crystal structure of the DAP BII hexapeptide complex I

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

VAL-TYR-ILE-HIS-PRO.1: 21 residues within 4Å: Chain A: G.45, C.46, A.62, N.191, W.192, R.196, D.200, G.250, N.306, T.307, L.553, I.628, T.629, G.630, G.631, N.632, S.633, F.649, D.650, G.651, S.655 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:A.62, A:W.192, A:W.192, A:I.628, A:I.628 Hydrogen bonds: A:G.45, A:N.191, A:N.191, A:N.306, A:G.631, A:S.633, A:S.633, A:F.649, A:S.655 Water bridges: A:I.628, A:V.656 VAL-TYR-ILE-HIS-PRO.2: 21 residues within 4Å: Chain B: G.45, C.46, A.62, N.191, W.192, R.196, D.200, G.250, N.306, T.307, L.553, I.628, T.629, G.630, G.631, N.632, S.633, F.649, D.650, G.651, S.655 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:A.62, B:W.192, B:W.192, B:I.628, B:I.628 Hydrogen bonds: B:G.45, B:N.191, B:N.306, B:N.306, B:G.631, B:S.633, B:S.633, B:F.649, B:D.650, B:S.655, B:S.655 Water bridges: B:T.307

12 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 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:I.615, B:D.569, B:G.570, B:M.571 GOL.4: 5 residues within 4Å: Chain A: D.35, K.227, H.228, W.229, K.231 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.228, A:H.228, A:W.229, A:W.229 GOL.5: 4 residues within 4Å: Chain A: G.44, F.101, R.151, 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.44 GOL.6: 7 residues within 4Å: Chain A: Y.65, K.184, D.188, A.298, M.301, A.302, N.305 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.65, A:K.184, A:A.298, A:M.301, A:A.302, A:N.305 Water bridges: A:N.306 GOL.7: 6 residues within 4Å: Chain A: C.63, A.64, G.66, A.67, A.98, Y.204 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.66, A:A.67 Water bridges: A:C.63, A:R.99, A:Y.204, A:Q.419, A:Q.419, A:R.423 GOL.8: 5 residues within 4Å: Chain A: R.389, 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.9: 3 residues within 4Å: Chain A: N.77, Q.294, V.295 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.77, A:N.77, A:Q.294, A:Q.294 GOL.10: 7 residues within 4Å: Chain A: A.233, D.234, Q.235, P.236, G.609, L.610, R.675 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.234, A:G.609 Water bridges: A:Q.235, A:R.675, A:R.678 GOL.13: 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, A:M.571, B:T.574, B:I.615 GOL.14: 7 residues within 4Å: Chain B: T.33, L.103, D.104, F.148, L.167, Y.224, K.227 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.224 Water bridges: B:Y.224 GOL.15: 5 residues within 4Å: Chain B: D.35, K.227, H.228, W.229, K.231 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.227, B:H.228, B:W.229, B:W.229 GOL.16: 4 residues within 4Å: Chain B: G.44, F.101, R.151, N.166 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.151, B:N.166 Water bridges: B:G.45, B:Y.153

4 x ZN: ZINC ION(Non-covalent)

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.21 ZN.12: 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.37

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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