SMTL ID : 3dba.1 (2 other biounits)

Crystal structure of the cGMP-bound GAF a domain from the photoreceptor phosphodiesterase 6C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

homo-tetramer

Ligands

4 x 35G: GUANOSINE-3',5'-MONOPHOSPHATE(Non-covalent)

35G.1: 19 residues within 4Å: Chain A: R.42, S.44, F.46, L.62, N.63, F.83, G.88, I.89, A.90, H.110, F.111, S.112, L.115, D.116, T.119, Y.121, T.123, M.142, L.144 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.44, A:N.63, A:N.63, A:I.89, A:A.90, A:S.112, A:T.119, A:T.119, A:T.123 Water bridges: B:E.155 35G.5: 19 residues within 4Å: Chain B: C.43, S.44, F.46, L.62, N.63, F.83, G.88, I.89, A.90, F.111, S.112, L.115, D.116, T.119, Y.121, T.123, M.126, M.142, L.144 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.44, B:N.63, B:N.63, B:I.89, B:A.90, B:S.112, B:T.119, B:T.119, B:T.123 Water bridges: B:N.63, B:G.88, B:G.91, B:D.116 35G.8: 19 residues within 4Å: Chain C: R.42, S.44, F.46, L.62, N.63, F.83, G.88, I.89, A.90, H.110, F.111, S.112, L.115, D.116, T.119, Y.121, T.123, M.142, L.144 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.44, C:N.63, C:N.63, C:I.89, C:A.90, C:S.112, C:T.119 35G.12: 19 residues within 4Å: Chain D: C.43, S.44, F.46, L.62, N.63, F.83, G.88, I.89, A.90, F.111, S.112, L.115, D.116, T.119, Y.121, T.123, M.126, M.142, L.144 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:S.44, D:N.63, D:N.63, D:I.89, D:A.90, D:S.112, D:T.119 Water bridges: D:N.63, D:G.88, D:G.91, D:D.116

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: V.82, Y.114 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.82, A:Y.114 Water bridges: A:V.82, A:S.112 GOL.3: 4 residues within 4Å: Chain A: W.92, K.98, F.100, H.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.98, A:K.98, A:H.110 GOL.4: 5 residues within 4Å: Chain A: H.28, K.29, Q.32, S.68, F.70 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.29, A:Q.32, A:Q.32, A:F.70 Water bridges: A:E.71 GOL.6: 3 residues within 4Å: Chain B: T.81, V.82, F.83 No protein-ligand interaction detected (PLIP) GOL.7: 5 residues within 4Å: Chain B: H.28, Q.32, S.68, K.69, F.70 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.28, B:Q.32, B:F.70 Water bridges: B:E.71 GOL.9: 2 residues within 4Å: Chain C: V.82, Y.114 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:V.82, C:Y.114 Water bridges: C:V.82, C:S.112 GOL.10: 4 residues within 4Å: Chain C: W.92, K.98, F.100, H.110 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.98, C:K.98, C:H.110 GOL.11: 5 residues within 4Å: Chain C: H.28, K.29, Q.32, S.68, F.70 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:H.28, C:K.29, C:Q.32, C:Q.32, C:F.70 Water bridges: C:E.71 GOL.13: 3 residues within 4Å: Chain D: T.81, V.82, F.83 No protein-ligand interaction detected (PLIP) GOL.14: 5 residues within 4Å: Chain D: H.28, Q.32, S.68, K.69, F.70 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.28, D:Q.32, D:F.70 Water bridges: D:E.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martinez, S.E. et al., The Structure of the GAF A Domain from Phosphodiesterase 6C Reveals Determinants of cGMP Binding, a Conserved Binding Surface, and a Large cGMP-dependent Conformational Change. J.Biol.Chem. (2008)

Release Date

2008-07-01

Peptides

Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha': ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'

Related Entries With Identical Sequence