SMTL ID : 1ptw.1

The Crystal Structure of AMP-Bound PDE4 Suggests a Mechanism for Phosphodiesterase Catalysis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.86, H.122, D.123, D.240 Ligands: AMP.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.86, A:H.122, A:D.123, A:D.240, AMP.3 ZN.2: 3 residues within 4Å: Chain A: D.123, H.155 Ligands: AMP.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.123, H2O.1, H2O.1, H2O.1 ZN.4: 6 residues within 4Å: Chain B: H.86, H.122, D.123, D.240 Ligands: ZN.5, AMP.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.86, B:H.122, B:D.123, B:D.240 ZN.5: 4 residues within 4Å: Chain B: D.123, H.155 Ligands: ZN.4, AMP.6 5 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:D.123, H2O.2, H2O.2, H2O.2, AMP.6 ZN.7: 6 residues within 4Å: Chain C: H.86, H.122, D.123, D.240 Ligands: ZN.8, AMP.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.86, C:H.122, C:D.123, C:D.240 ZN.8: 4 residues within 4Å: Chain C: H.122, D.123 Ligands: ZN.7, AMP.9 5 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: C:D.123, H2O.2, H2O.2, H2O.2, AMP.9 ZN.10: 6 residues within 4Å: Chain D: H.86, H.122, D.123, D.240 Ligands: ZN.11, AMP.12 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.86, D:H.122, D:D.123, D:D.240 ZN.11: 4 residues within 4Å: Chain D: H.122, D.123 Ligands: ZN.10, AMP.12 5 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: D:D.123, H2O.3, H2O.3, H2O.3, AMP.12

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 14 residues within 4Å: Chain A: Y.81, H.82, H.86, H.122, D.123, D.240, L.241, N.243, I.258, F.262, Q.291, F.294 Ligands: ZN.1, ZN.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:H.82, A:D.123, A:N.243, A:N.243, A:Q.291 Water bridges: A:Y.81, A:T.193 Salt bridges: A:H.82, A:H.86 pi-Stacking: A:F.294 AMP.6: 15 residues within 4Å: Chain B: Y.81, H.82, H.122, D.123, M.195, D.240, L.241, N.243, T.255, I.258, F.262, Q.291, F.294 Ligands: ZN.4, ZN.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.123, B:D.123, B:N.243, B:T.255, B:Q.291 Salt bridges: B:H.82 pi-Stacking: B:F.294 AMP.9: 16 residues within 4Å: Chain C: Y.81, H.82, H.86, H.122, D.123, M.195, D.240, L.241, N.243, T.255, I.258, F.262, Q.291, F.294 Ligands: ZN.7, ZN.8 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:H.82, C:D.123, C:N.243, C:T.255, C:Q.291 Water bridges: C:Y.81 Salt bridges: C:H.82 pi-Stacking: C:F.294, C:F.294 AMP.12: 15 residues within 4Å: Chain D: Y.81, H.82, H.122, D.123, H.126, M.195, D.240, L.241, N.243, T.255, I.258, Q.291, F.294 Ligands: ZN.10, ZN.11 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:H.126, D:N.243, D:T.255, D:Q.291 Water bridges: D:H.82 Salt bridges: D:H.82, D:H.86 pi-Stacking: D:F.294

Links

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Citation

Huai, Q. et al., The crystal structure of AMP-bound PDE4 suggests a mechanism for phosphodiesterase catalysis. Biochemistry (2003)

Release Date

2003-11-11

Peptides

cAMP-specific phosphodiesterase PDE4D2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

cAMP-specific phosphodiesterase PDE4D2

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