SMTL ID : 5ojz.1

D10N variant of beta-phosphoglucomutase from Lactococcus lactis inhibited by a beryllium triflouride phosphoenzyme analogue to 1.3A resolution.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

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

MG.1: 5 residues within 4Å: Chain A: D.8, N.10, E.169, D.170 Ligands: BEF.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.8, A:N.10, A:D.170, H2O.2, H2O.5 MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Covalent)

BEF.3: 7 residues within 4Å: Chain A: D.8, L.9, N.10, S.114, A.115, K.145 Ligands: MG.1 No protein-ligand interaction detected (PLIP)

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 6 residues within 4Å: Chain A: S.163, G.182, A.183, L.184, W.216, K.219 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.163, A:K.219 EDO.5: 3 residues within 4Å: Chain A: V.201, H.206, F.211 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.206, A:H.206 EDO.6: 5 residues within 4Å: Chain A: T.129, F.132, D.133, A.134, I.135 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.133 EDO.7: 2 residues within 4Å: Chain A: E.140 Ligands: EDO.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.140 EDO.8: 3 residues within 4Å: Chain A: D.137, E.140 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.137 EDO.9: 5 residues within 4Å: Chain A: A.17, E.18, R.38, N.41, K.45 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.38, A:K.45 Water bridges: A:R.38, A:N.41 EDO.10: 7 residues within 4Å: Chain A: K.25, A.28, E.29, I.33, N.34, G.35, V.36 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.33, A:V.36 Water bridges: A:G.35, A:G.35, A:G.35 EDO.11: 6 residues within 4Å: Chain A: A.115, P.138, V.141, S.144, K.145, I.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.145 Water bridges: A:K.117 EDO.12: 5 residues within 4Å: Chain A: Y.93, P.94, V.188, D.203, T.204 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.204 EDO.13: 3 residues within 4Å: Chain A: S.88, P.89, A.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.88, A:A.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, L.A. et al., van der Waals Contact between Nucleophile and Transferring Phosphorus Is Insufficient To Achieve Enzyme Transition-State Architecture. Acs Catalysis (2018)

Release Date

2018-08-29

Peptides

Beta-phosphoglucomutase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-phosphoglucomutase