SMTL ID : 2x14.1

The catalytically active fully closed conformation of human phosphoglycerate kinase K219A mutant in complex with AMP-PCP and 3PG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: K.215, D.374 Ligands: ACP.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.374, H2O.8, H2O.9

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

3PG.2: 12 residues within 4Å: Chain A: D.23, N.25, R.38, H.62, R.65, R.122, G.166, T.167, H.169, R.170, K.215 Ligands: ACP.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:D.23, A:N.25, A:R.38, A:G.166 Water bridges: A:R.65, A:R.170, A:R.170, A:K.215, A:K.215, A:G.373, A:G.395, A:G.396 Salt bridges: A:R.38, A:H.62, A:R.65, A:R.122, A:R.170, A:K.215, A:K.215

1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.3: 25 residues within 4Å: Chain A: R.38, G.213, A.214, K.215, G.237, G.238, F.241, L.256, G.312, L.313, N.336, G.337, P.338, G.340, V.341, E.343, G.371, G.372, G.373, D.374, T.375, G.395, G.396 Ligands: MG.1, 3PG.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:R.38, A:A.214, A:K.215, A:K.215, A:G.238, A:G.312, A:G.337, A:E.343, A:G.373, A:D.374, A:T.375, A:G.396 Water bridges: A:R.38, A:K.215, A:N.336, A:N.336, A:D.374, A:D.374, A:G.395 Salt bridges: A:K.215

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

2010-12-29

Peptides

PHOSPHOGLYCERATE KINASE 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PHOSPHOGLYCERATE KINASE 1