SMTL ID : 5eyh.1

Crystal Structure of IMPase/NADP phosphatase complexed with NADP and Ca2+ at pH 7.0

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

5 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.70, D.88, I.90 Ligands: CA.2, CA.5, NAP.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.70, A:D.88, A:I.90, H2O.1, H2O.1 CA.2: 4 residues within 4Å: Chain A: K.36, E.70 Ligands: CA.1, NAP.6 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.70, H2O.1, H2O.1, H2O.1, H2O.3 CA.5: 5 residues within 4Å: Chain A: D.88, D.91, D.209 Ligands: CA.1, NAP.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.88, A:D.91, A:D.209 CA.7: 5 residues within 4Å: Chain B: D.88, D.91, D.209 Ligands: CA.8, NAP.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.88, B:D.91, B:D.209, H2O.6 CA.8: 5 residues within 4Å: Chain B: E.70, D.88, I.90 Ligands: CA.7, NAP.9 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.70, B:D.88, B:I.90, H2O.5, H2O.5

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: E.34, T.35, K.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.35, A:K.36 GOL.4: 5 residues within 4Å: Chain A: F.173, D.174, S.176, F.177 Chain B: Q.162 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.162, A:F.177 Water bridges: B:Q.162

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.6: 22 residues within 4Å: Chain A: H.38, F.40, E.70, D.88, I.90, D.91, G.92, T.93, N.160, V.163, G.183, A.184, C.185, N.202, T.203, N.204, D.209 Chain B: S.178, R.180 Ligands: CA.1, CA.2, CA.5 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:V.163 Hydrogen bonds: A:G.92, A:T.93, A:N.160, A:C.185, A:N.202, A:N.204, B:S.178 Water bridges: A:T.93, A:A.94, A:T.203, A:T.203, B:R.180, B:R.180 Salt bridges: B:R.180 NAP.9: 20 residues within 4Å: Chain A: S.178, R.180 Chain B: E.70, D.88, I.90, D.91, G.92, T.93, A.94, N.160, V.163, G.183, A.184, C.185, N.202, T.203, N.204, D.209 Ligands: CA.7, CA.8 20 PLIP interactions: 4 interactions with chain A, 16 interactions with chain B Hydrogen bonds: A:S.178, B:D.91, B:G.92, B:T.93, B:T.93, B:N.160, B:C.185, B:N.202, B:T.203, B:T.203, B:N.204 Water bridges: A:R.180, A:R.180, B:A.94, B:A.94, B:A.94, B:N.160, B:N.160 Salt bridges: A:R.180 Hydrophobic interactions: B:N.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhattacharyya, S. et al., Structural elucidation of the NADP(H) phosphatase activity of staphylococcal dual-specific IMPase/NADP(H) phosphatase. Acta Crystallogr D Struct Biol (2016)

Release Date

2015-12-23

Peptides

Inositol monophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Inositol monophosphatase

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