SMTL ID : 3zlb.1

Crystal structure of phosphoglycerate kinase from Streptococcus pneumoniae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

monomer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 7 residues within 4Å: Chain A: M.1, K.3, L.4, T.5, D.8, K.398 Ligands: GOL.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.8 MG.2: 2 residues within 4Å: Chain A: G.287, E.288 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.288, H2O.11, H2O.12, H2O.16 MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain A: D.356 Ligands: ANP.3 No protein-ligand interaction detected (PLIP)

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.3: 23 residues within 4Å: Chain A: G.202, S.203, K.208, G.226, G.227, Y.230, L.244, F.276, G.296, L.297, N.320, G.321, P.322, G.324, V.325, F.326, E.327, G.354, G.355, D.356, S.357, M.381 Ligands: MG.9 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:S.203, A:K.208, A:G.227, A:G.296, A:N.320, A:N.320, A:G.321, A:E.327, A:G.354, A:G.355, A:D.356, A:S.357, A:S.357 Water bridges: A:S.203, A:K.204, A:K.204, A:G.226, A:E.327 Salt bridges: A:K.208

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: A.83, G.86 No protein-ligand interaction detected (PLIP) GOL.5: 7 residues within 4Å: Chain A: M.1, T.5, K.7, D.8, E.179, K.398 Ligands: MG.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.1, A:T.5, A:D.8, A:K.398 GOL.6: 11 residues within 4Å: Chain A: D.21, R.36, D.150, A.151, F.152, G.153, L.177, E.181, S.374, T.375, G.376 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.21, A:G.153, A:E.181, A:T.375, A:T.375 Water bridges: A:R.36, A:F.152, A:F.152 GOL.7: 7 residues within 4Å: Chain A: A.78, A.79, A.82, D.88, V.89, V.90, F.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.89, A:V.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fulde, M. et al., Pneumococcal phosphoglycerate kinase interacts with plasminogen and its tissue activator. Thromb. Haemost. (2014)

Release Date

2014-02-12

Peptides

PHOSPHOGLYCERATE KINASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PHOSPHOGLYCERATE KINASE