SMTL ID : 5xsn.1

The catalytic domain of GdpP with c-di-AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: D.37, D.106, H.130, H.131, D.185 Ligands: MN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.37, A:D.106, A:H.130, A:D.185, H2O.1 MN.2: 4 residues within 4Å: Chain A: H.31, D.35, D.106 Ligands: MN.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.31, A:D.35, A:D.106, H2O.1 MN.4: 5 residues within 4Å: Chain B: D.37, D.106, H.130, D.185 Ligands: MN.5 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.37, B:D.106, B:D.106, B:H.130, B:D.185 MN.5: 4 residues within 4Å: Chain B: H.31, D.35, D.106 Ligands: MN.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.31, B:D.35, B:D.35, B:D.106

2 x 2BA: (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide(Non-covalent)

2BA.3: 14 residues within 4Å: Chain A: R.187, P.255, V.256, A.259, Q.260, S.288, R.290, G.306, G.307, G.308, N.312, A.313, A.314, Q.316 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.260, A:A.313, A:Q.316, A:Q.316 Water bridges: A:R.187, A:R.187 Salt bridges: A:R.290 2BA.6: 13 residues within 4Å: Chain B: P.255, V.256, A.259, Q.260, S.288, R.290, G.306, G.307, G.308, N.312, A.313, A.314, Q.316 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.260, B:A.313, B:Q.316, B:Q.316 Water bridges: B:R.280, B:R.280, B:R.290, B:T.315 Salt bridges: B:R.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, F. et al., Structural and biochemical characterization of the catalytic domains of GdpP reveals a unified hydrolysis mechanism for the DHH/DHHA1 phosphodiesterase. Biochem. J. (2018)

Release Date

2018-01-31

Peptides

Phosphodiesterase acting on cyclic dinucleotides: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phosphodiesterase acting on cyclic dinucleotides

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