SMTL ID : 2yoz.1

Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, crystallized with 2'-AMPS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x OVE: 2'-O-(sulfidophosphinato)adenosine(Non-covalent)

OVE.1: 13 residues within 4Å: Chain A: L.10, Y.11, H.73, T.75, F.78, R.150, H.152, T.154, P.163, V.164, T.166, G.167 Ligands: ACT.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:H.73, A:H.152, A:T.154, A:T.154, A:V.164 Water bridges: A:T.75, A:T.75, A:F.78, A:T.154, A:T.154, A:T.166 pi-Stacking: A:F.78

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: T.23, R.191, K.208, K.209, M.210, E.211 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.191, A:R.191, A:E.211 Water bridges: A:K.208

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.3: 8 residues within 4Å: Chain A: K.39, A.40, K.43, E.44, H.47, V.186, S.196, W.202 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.43

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

ACT.4: 10 residues within 4Å: Chain A: F.41, L.45, L.58, L.60, Y.63, F.64, V.113, T.114, P.115, G.200 No protein-ligand interaction detected (PLIP) ACT.5: 6 residues within 4Å: Chain A: K.66, R.67, P.68, P.69, C.157 Ligands: OVE.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.67 ACT.6: 4 residues within 4Å: Chain A: K.102, A.103, F.104, K.105 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.103 Salt bridges: A:K.105 ACT.8: 1 residues within 4Å: Chain A: K.213 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.213, A:K.213, A:K.213, A:K.213 Salt bridges: A:K.213

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 7 residues within 4Å: Chain A: W.132, L.136, P.139, S.140, G.148, S.149, R.150 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Myllykoski, M. et al., Crystallographic Analysis of the Reaction Cycle of 2',3'-Cyclic Nucleotide 3'-Phosphodiesterase, a Unique Member of the 2H Phosphoesterase Family. J.Mol.Biol. (2013)

Release Date

2013-07-10

Peptides

2,3-CYCLIC NUCLEOTIDE 3'-PHOSPHODIESTERASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

2,3-CYCLIC NUCLEOTIDE 3'-PHOSPHODIESTERASE

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