SMTL ID : 3cww.1

Crystal Structure of IDE-bradykinin complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-dimer

Ligands

2 x ALA- PRO- PRO- ALA: bradykinin N-terminal tetrapeptide analogue(Non-covalent)

ALA-PRO-PRO-ALA.1: 8 residues within 4Å: Chain B: G.310, E.312, L.330, V.331, G.332, G.333, Q.334, Y.580 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.331 Hydrogen bonds: B:E.312, B:E.312, B:G.332 ALA-PRO-PRO-ALA.2: 9 residues within 4Å: Chain A: G.306, G.310, E.312, L.330, V.331, G.332, G.333, Q.334, Y.580 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.331 Hydrogen bonds: A:E.312, A:G.332

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: H.79, H.83, E.160 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.79, A:H.83, A:E.160, A:E.160 ZN.8: 3 residues within 4Å: Chain B: H.79, H.83, E.160 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.79, B:H.83, B:E.160, B:E.160

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 4 residues within 4Å: Chain A: P.71, N.73, E.211, K.214 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.73 Salt bridges: A:K.214 ACT.5: 4 residues within 4Å: Chain A: N.283, T.329, V.331, N.347 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.347 Hydrogen bonds: A:T.329, A:N.347, A:D.349 ACT.9: 6 residues within 4Å: Chain B: N.300, H.303, N.389, E.424, Y.425, L.427 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.300, B:N.389, B:Y.425 Salt bridges: B:H.303 ACT.10: 7 residues within 4Å: Chain B: L.659, A.665, T.667, E.670, M.966, T.967, K.970 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:M.966 Hydrogen bonds: B:L.659 Water bridges: B:A.665, B:A.665 Salt bridges: B:K.970

5 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.6: 5 residues within 4Å: Chain A: Q.771, E.881, S.884, Q.886, R.891 No protein-ligand interaction detected (PLIP) DIO.7: 7 residues within 4Å: Chain A: L.172, L.175, E.176, T.179, Y.273, R.448, A.450 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.448, A:A.450 DIO.11: 6 residues within 4Å: Chain B: L.172, L.175, E.176, T.179, R.448, A.450 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.179 Water bridges: B:T.287, B:R.448 DIO.12: 4 residues within 4Å: Chain B: E.881, S.884, Q.886, R.891 No protein-ligand interaction detected (PLIP) DIO.13: 5 residues within 4Å: Chain B: Y.656, L.659, D.669, Y.750, Q.752 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.750

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malito, E. et al., Molecular Bases for the Recognition of Short Peptide Substrates and Cysteine-Directed Modifications of Human Insulin-Degrading Enzyme. Biochemistry (2008)

Release Date

2008-11-25

Peptides

Insulin-degrading enzyme: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Insulin-degrading enzyme