SMTL ID : 4axx.1

The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with ADP 3-phosphoglycerate and beryllium trifluoride

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: K.216, D.375 Ligands: ADP.3, BEF.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.375, H2O.10, H2O.15

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

CL.2: 5 residues within 4Å: Chain A: R.66, K.216, V.217, A.218, D.219 Ligand excluded by PLIP

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 23 residues within 4Å: Chain A: G.214, A.215, K.216, K.220, G.238, G.239, F.242, L.257, G.313, L.314, N.337, P.339, G.341, V.342, E.344, G.372, G.373, G.374, D.375, T.376, G.396 Ligands: MG.1, BEF.5 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:A.215, A:K.216, A:G.239, A:G.313, A:N.337, A:E.344, A:G.372, A:G.374, A:D.375, A:T.376 Water bridges: A:D.375, A:D.375 Salt bridges: A:K.216, A:K.220, A:K.220

1 x 3PG: 3-PHOSPHOGLYCERIC ACID(Non-covalent)

3PG.4: 12 residues within 4Å: Chain A: D.24, N.26, R.39, H.63, R.66, R.123, G.167, T.168, H.170, R.171, K.216 Ligands: BEF.5 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:D.24, A:N.26, A:R.39, A:R.39 Water bridges: A:R.123, A:R.123, A:G.167, A:H.170, A:K.216, A:K.216, A:K.216, A:G.374, A:G.397 Salt bridges: A:R.39, A:H.63, A:R.66, A:R.123, A:R.171, A:K.216, A:K.216

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.5: 11 residues within 4Å: Chain A: R.39, K.216, K.220, G.373, G.374, D.375, G.396, G.397 Ligands: MG.1, ADP.3, 3PG.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pellegrini, E. et al., Metal fluorides-multi-functional tools for the study of phosphoryl transfer enzymes, a practical guide. Structure (2024)

Release Date

2013-06-26

Peptides

PHOSPHOGLYCERATE KINASE 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PHOSPHOGLYCERATE KINASE 1