SMTL ID : 6vck.1

Crystal structure of E.coli RppH-DapF in complex with GDP, Mg2+ and F-

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

hetero-1-1-mer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain B: R.53, E.54 Ligands: MG.2, GDP.4, F.6 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.54, H2O.3 MG.2: 7 residues within 4Å: Chain B: E.54, E.58, E.121 Ligands: MG.1, MG.3, GDP.4, F.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.54, B:E.121 MG.3: 4 residues within 4Å: Chain B: Q.38, E.121 Ligands: MG.2, GDP.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:Q.38, B:E.121, B:E.121

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.4: 17 residues within 4Å: Chain B: N.11, R.28, Q.35, Q.38, G.39, G.40, E.54, Y.78, L.80, Q.96, E.121, F.140, K.141 Ligands: MG.1, MG.2, MG.3, F.6 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.11, B:R.28, B:R.28, B:Q.38, B:Q.38, B:G.40, B:Q.96, B:K.141 Water bridges: B:R.53, B:E.54 pi-Cation interactions: B:R.28, B:R.28

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

CL.5: 2 residues within 4Å: Chain B: S.62, R.63 Ligand excluded by PLIP

1 x F: FLUORIDE ION(Non-covalent)

F.6: 6 residues within 4Å: Chain B: E.54, E.57, E.121 Ligands: MG.1, MG.2, GDP.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, A. et al., Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH. Nucleic Acids Res. (2020)

Release Date

2020-02-05

Peptides

Diaminopimelate epimerase: A
RNA pyrophosphohydrolase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Diaminopimelate epimerase

RNA pyrophosphohydrolase

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