SMTL ID : 5a7i.1

Crystal structure of INPP5B in complex with biphenyl 3,3',4,4',5,5'- hexakisphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: G.115, I.116, M.117, R.153 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.117, A:G.118, A:R.153, A:R.153

1 x B6K: Biphenyl 3,3',4,4',5,5'-hexakisphosphate(Non-covalent)

B6K.2: 9 residues within 4Å: Chain A: M.1, H.308, H.309, H.310, H.311, H.312, H.313 Ligands: PO4.3, MG.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:M.1, A:M.1, A:H.309, A:H.311, A:H.312 Water bridges: A:H.311, A:H.311 Salt bridges: A:H.308, A:H.309, A:H.309, A:H.310, A:H.311, A:H.311, A:H.311, A:H.312, A:H.312, A:H.313

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 2 residues within 4Å: Ligands: B6K.2, MG.4 No protein-ligand interaction detected (PLIP) PO4.5: 5 residues within 4Å: Chain A: Y.216, K.222, V.225, E.236, R.268 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.236, A:R.268 Water bridges: A:K.222 PO4.6: 3 residues within 4Å: Chain A: G.113, R.119, R.164 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.113, A:G.113 Salt bridges: A:R.164

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.4: 2 residues within 4Å: Ligands: B6K.2, PO4.3 No protein-ligand interaction detected (PLIP)

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

CL.7: 3 residues within 4Å: Chain A: K.81, K.83, L.84 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mills, S.J. et al., Crystal Structures of Type-II Inositol Polyphosphate 5-Phosphatase Inpp5B with Synthetic Inositol Polyphosphate Surrogates Reveal New Mechanistic Insights for the Inositol 5-Phosphatase Family. Biochemistry (2016)

Release Date

2016-04-13

Peptides

TYPE II INOSITOL 1,4,5-TRISPHOSPHATE 5-PHOSPHATASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

TYPE II INOSITOL 1,4,5-TRISPHOSPHATE 5-PHOSPHATASE

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