SMTL ID : 5eyg.1

Crystal structure of IMPase/NADP phosphatase complexed with NADP and Ca2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.88, D.91, D.209 Ligands: CA.2, NAP.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.88, A:D.91, A:D.209, H2O.3 CA.2: 6 residues within 4Å: Chain A: E.70, D.88, I.90, T.93 Ligands: CA.1, NAP.8 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.3 CA.9: 5 residues within 4Å: Chain B: D.88, D.91, D.209 Ligands: CA.10, NAP.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.88, B:D.91, B:D.209, H2O.8 CA.10: 5 residues within 4Å: Chain B: E.70, D.88, I.90 Ligands: CA.9, NAP.12 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.88, B:I.90, H2O.7, H2O.8, H2O.8

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 7 residues within 4Å: Chain A: Q.66, K.72, S.73, N.74, A.75, M.76, I.77 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.72, A:A.75, A:M.76 Water bridges: A:L.67, A:L.67, A:S.73 PGE.4: 6 residues within 4Å: Chain A: C.139, F.142, K.143, M.144, E.145, K.194 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.142, A:E.145 PGE.6: 10 residues within 4Å: Chain A: M.1, T.5, I.9, F.62, P.63, E.64, H.65, H.83, Y.109, Y.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.64, A:Y.109

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: V.97, K.98, Q.100 Chain B: P.148, K.194, G.195, Q.196 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.99, A:Q.100 GOL.13: 7 residues within 4Å: Chain A: K.194, G.195, Q.196 Chain B: V.97, K.98, Q.99, Q.100 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.97, B:Q.99, B:Q.100 Water bridges: B:R.39, B:R.39, B:R.39, A:K.194

1 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.7: 12 residues within 4Å: Chain A: E.101, D.102, H.125, R.180, L.181, V.182, R.191 Chain B: D.102, H.125, L.181, V.182, R.191 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.181, A:R.191, B:R.191 Water bridges: A:H.125, A:R.191

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

NAP.8: 20 residues within 4Å: Chain A: 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 Chain B: S.178, R.180 Ligands: CA.1, CA.2 19 PLIP interactions: 4 interactions with chain B, 15 interactions with chain A Hydrogen bonds: B:S.178, B:R.180, A:G.92, A:T.93, A:N.160, A:C.185, A:N.202, A:T.203, A:T.203, A:N.204 Water bridges: B:S.178, A:T.93, A:A.94, A:A.94, A:N.160, A:N.160, A:N.160 Salt bridges: B:R.180 Hydrophobic interactions: A:N.160 NAP.12: 20 residues within 4Å: Chain A: F.177, S.178, R.180 Chain B: 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.9, CA.10 21 PLIP interactions: 5 interactions with chain A, 16 interactions with chain B Hydrogen bonds: A:S.178, A:S.178, B:I.90, B:G.92, B:T.93, B:T.93, B:A.94, 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:N.95, B:N.160, B:N.160, B:D.209 Salt bridges: A:R.180 Hydrophobic interactions: B:N.160

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.11: 5 residues within 4Å: Chain B: Q.7, Q.8, K.11, L.12, S.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.15, B:S.15

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

CL.14: 2 residues within 4Å: Chain B: L.187, R.191 Ligand excluded by PLIP

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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