SMTL ID : 6y8y.1

Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5) with bound Glucose-1-Phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 4 residues within 4Å: Chain A: S.143, D.314, D.316, D.318 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.143, A:D.314, A:D.316, A:D.318, H2O.1

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: C.481, V.494 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:C.481, A:V.494, H2O.1, H2O.7, H2O.9

1 x G1P: 1-O-phosphono-alpha-D-glucopyranose(Non-covalent)

G1P.3: 16 residues within 4Å: Chain A: T.45, N.46, S.143, R.319, G.384, E.402, E.403, S.404, K.415, R.529, S.531, G.532, T.533, R.542 Ligands: GOL.8, NA.12 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.46, A:R.319, A:E.402, A:S.404, A:K.415, A:R.529, A:G.532, A:T.533, A:T.533, A:R.542 Water bridges: A:E.402, A:E.402 Salt bridges: A:R.529, A:R.542, A:R.542

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: F.55, E.56, Q.63, F.92 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.63 Water bridges: A:K.58, A:Y.61, A:Q.63 GOL.5: 7 residues within 4Å: Chain A: F.328, R.440, R.448, N.556, R.557, E.558, P.559 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.448, A:R.448 GOL.6: 2 residues within 4Å: Chain A: Y.466, D.470 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.470, A:D.470 GOL.7: 2 residues within 4Å: Chain A: A.377, V.378 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.378, A:V.378 GOL.8: 8 residues within 4Å: Chain A: R.144, D.289, N.291, R.319, S.404, R.453, R.542 Ligands: G1P.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.144, A:R.144, A:D.289, A:N.291, A:R.319, A:R.319, A:R.453, A:R.542, A:R.542 Water bridges: A:R.453, A:E.457 GOL.9: 9 residues within 4Å: Chain A: V.30, Q.79, A.105, A.106, G.108, L.203, E.204, N.205, K.206 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.79, A:A.105, A:G.108, A:E.204, A:K.206 Water bridges: A:N.205

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 4 residues within 4Å: Chain A: Y.294, A.295, T.296, G.297 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.296, A:T.296, A:G.297 Water bridges: A:N.276, A:L.298 Salt bridges: A:H.286

5 x NA: SODIUM ION(Non-functional Binders)

NA.11: 2 residues within 4Å: Chain A: D.282, G.285 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.282, A:D.282 NA.12: 5 residues within 4Å: Chain A: R.49, S.143, R.319, T.533 Ligands: G1P.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.49, A:R.49, A:R.319, A:T.533 NA.13: 3 residues within 4Å: Chain A: Q.433, G.434, D.437 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.434 Water bridges: A:Q.433, A:D.437, A:D.437 NA.14: 5 residues within 4Å: Chain A: E.24, P.27, D.202, L.203, K.206 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.24, A:L.203 Water bridges: A:L.203, A:N.205 NA.15: 3 residues within 4Å: Chain A: R.355, V.376, A.377 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.355, A:A.377

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gustafsson, R. et al., Structure and Characterization of Phosphoglucomutase 5 from Atlantic and Baltic Herring-An Inactive Enzyme with Intact Substrate Binding. Biomolecules (2020)

Release Date

2020-12-16

Peptides

Phosphoglucomutase 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphoglucomutase 5