SMTL ID : 5xsp.1

The catalytic domain of GdpP with 5'-pApA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: D.37, D.106, H.130, 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 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.31, A:D.35, A:D.35, A:D.106, H2O.1 MN.5: 5 residues within 4Å: Chain B: D.37, D.106, H.130, D.185 Ligands: MN.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.37, B:D.106, B:H.130, B:D.185, H2O.9 MN.6: 4 residues within 4Å: Chain B: H.31, D.35, D.106 Ligands: MN.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.31, B:D.35, B:D.35, B:D.106, H2O.9

4 x A: ADENOSINE-5'-MONOPHOSPHATE(Non-covalent)

A.3: 7 residues within 4Å: Chain A: R.187, P.255, V.256, A.259, Q.260, R.290 Ligands: A.4 19 PLIP interactions: 9 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:R.187, A:Q.260, A:S.288, A:N.312, A:Q.316, A:Q.316, B:Q.260, B:S.288, B:N.312, B:Q.316 Water bridges: A:R.290, A:R.290, B:A.259, B:R.290, B:R.290, B:G.305, B:Q.316 Salt bridges: A:R.290, B:R.290 A.4: 11 residues within 4Å: Chain A: S.288, R.290, G.306, G.307, G.308, H.309, N.312, A.313, A.314, Q.316 Ligands: A.3 Protein-ligand interaction information (PLIP) not available A.7: 6 residues within 4Å: Chain B: P.255, V.256, A.259, Q.260, R.290 Ligands: A.8 Protein-ligand interaction information (PLIP) not available A.8: 11 residues within 4Å: Chain B: S.288, R.290, G.306, G.307, G.308, H.309, N.312, A.313, A.314, Q.316 Ligands: A.7 Protein-ligand interaction information (PLIP) not available

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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