SMTL ID : 7p97.2 (1 other biounit)

Structure of 3-phospho-D-glycerate guanylyltransferase with product 3-GPPG bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

1 x 6WI: 3-(guanosine-5'-diphospho)-D-glycerate(Non-covalent)

6WI.1: 29 residues within 4Å: Chain A: P.45, L.46, K.47, K.53, F.69, V.92, T.93, P.94, P.113, P.114, D.115, E.116, G.117, M.118, A.121, P.141, G.142, D.143, G.173, T.174, N.175, F.188, S.189, S.192, D.218, D.220 Ligands: MG.2, MG.3, CL.4 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:P.45, A:L.46, A:K.47, A:V.92, A:D.115, A:E.116, A:G.117, A:G.142, A:T.174, A:S.189, A:S.192, A:D.218, A:D.220, A:D.220 Water bridges: A:K.47, A:K.47, A:K.47, A:P.113, A:M.118, A:N.168, A:N.168, A:G.190, A:D.218, A:D.218 Salt bridges: A:K.53

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: K.53, D.143, D.218, D.220 Ligands: 6WI.1, MG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.143, A:D.218, A:D.220, H2O.1 MG.3: 5 residues within 4Å: Chain A: N.168, D.218, D.220 Ligands: 6WI.1, MG.2 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.218, A:D.220, H2O.1, H2O.2, H2O.2

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

CL.4: 5 residues within 4Å: Chain A: K.47, A.52, K.53, F.69 Ligands: 6WI.1 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: N.198, A.199, R.202 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hasan, M. et al., Diversification by CofC and Control by CofD Govern Biosynthesis and Evolution of Coenzyme F 420 and Its Derivative 3PG-F 420. Mbio (2022)

Release Date

2022-02-02

Peptides

3-phospho-D-glycerate guanylyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BBB

3-phospho-D-glycerate guanylyltransferase

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