SMTL ID : 1mkd.2 (1 other biounit)

crystal structure of PDE4D catalytic domain and zardaverine complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.79, H.115, D.116, D.233 Ligands: MG.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.79, A:H.115, A:D.116, A:D.233 ZN.4: 5 residues within 4Å: Chain B: H.79, H.115, D.116, D.233 Ligands: MG.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.79, B:H.115, B:D.116, B:D.233 ZN.7: 5 residues within 4Å: Chain C: H.79, H.115, D.116, D.233 Ligands: MG.8 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.79, C:H.115, C:D.116, C:D.233 ZN.10: 5 residues within 4Å: Chain D: H.79, H.115, D.116, D.233 Ligands: MG.11 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.79, D:H.115, D:D.116, D:D.233 ZN.13: 4 residues within 4Å: Chain E: H.79, H.115, D.116, D.233 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:H.79, E:H.115, E:D.116, E:D.233, E:D.233 ZN.16: 4 residues within 4Å: Chain F: H.79, H.115, D.116, D.233 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.79, F:H.115, F:D.116, F:D.233

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: H.115, D.116, E.145, T.186 Ligands: ZN.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.116 MG.5: 4 residues within 4Å: Chain B: D.116, E.145, T.186 Ligands: ZN.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.116 MG.8: 5 residues within 4Å: Chain C: H.115, D.116, E.145, T.186 Ligands: ZN.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.116 MG.11: 5 residues within 4Å: Chain D: H.115, D.116, E.145, T.186 Ligands: ZN.10 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.116 MG.14: 5 residues within 4Å: Chain E: H.115, D.116, E.145, H.148, T.186 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.116 MG.17: 5 residues within 4Å: Chain F: H.115, D.116, E.145, H.148, T.186 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.116

6 x ZAR: 6-(4-DIFLUOROMETHOXY-3-METHOXY-PHENYL)-2H-PYRIDAZIN-3-ONE(Non-covalent)

ZAR.3: 11 residues within 4Å: Chain A: Y.74, M.188, N.236, P.237, Y.244, W.247, T.248, I.251, M.272, Q.284, F.287 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.251 Hydrogen bonds: A:Q.284 pi-Stacking: A:F.287 ZAR.6: 12 residues within 4Å: Chain B: Y.74, M.188, N.236, P.237, Y.244, W.247, T.248, I.251, F.255, M.272, Q.284, F.287 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.251 Hydrogen bonds: B:Q.284 pi-Stacking: B:F.287 ZAR.9: 12 residues within 4Å: Chain C: Y.74, M.188, N.236, P.237, Y.244, W.247, T.248, I.251, F.255, M.272, Q.284, F.287 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.284 pi-Stacking: C:F.287 ZAR.12: 12 residues within 4Å: Chain D: Y.74, M.188, N.236, P.237, Y.244, W.247, T.248, I.251, F.255, M.272, Q.284, F.287 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.251 Hydrogen bonds: D:Q.284 pi-Stacking: D:F.287 ZAR.15: 12 residues within 4Å: Chain E: Y.74, M.188, N.236, P.237, Y.244, W.247, T.248, I.251, F.255, M.272, Q.284, F.287 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:I.251 Hydrogen bonds: E:Q.284 pi-Stacking: E:F.287 ZAR.18: 11 residues within 4Å: Chain F: Y.74, M.188, N.236, P.237, Y.244, W.247, T.248, I.251, M.272, Q.284, F.287 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:I.251 Hydrogen bonds: F:Q.284 pi-Stacking: F:F.287

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, M.E. et al., Crystal structure of phosphodiesterase 4D and inhibitor complex. FEBS LETT. (2002)

Release Date

2003-03-01

Peptides

Phosphodiesterase 4D: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
F

D
G

E
K

F
L

Phosphodiesterase 4D

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