SMTL ID : 3wop.1

Crystal structure of the DAP BII hexapeptide complex II

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

VAL-TYR-ILE-HIS-PRO.1: 20 residues within 4Å: Chain A: G.45, C.46, A.62, N.191, W.192, 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 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.62, A:W.192, A:W.192, 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 VAL-TYR-ILE-HIS-PRO.2: 20 residues within 4Å: Chain B: G.45, C.46, A.62, N.191, W.192, 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 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:W.192, B:W.192, 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:S.655, B:S.655 Water bridges: B:S.251, B:T.629

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: T.574, F.576, T.578, 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.35, A:H.228, A:W.229, A:W.229 GOL.5: 5 residues within 4Å: Chain A: N.77, I.79, K.80, Q.294, V.295 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.77 GOL.6: 8 residues within 4Å: Chain A: A.233, D.234, Q.235, P.236, G.609, L.610, R.675, R.678 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.233, A:D.234, A:G.609 GOL.9: 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.10: 8 residues within 4Å: Chain B: A.233, D.234, Q.235, P.236, G.609, L.610, R.675, R.678 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.609, B:R.678 Water bridges: B:Q.235, B:R.675 GOL.11: 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.12: 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.13: 6 residues within 4Å: Chain B: A.42, R.149, C.150, R.151, Y.153, N.166 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.149, B:R.151 Water bridges: B:G.45

4 x ZN: ZINC ION(Non-covalent)

ZN.7: 2 residues within 4Å: Chain A: E.481, K.484 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.481, A:E.481 ZN.8: 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.14 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.28 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.27

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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