SMTL ID : 6d13.1

Crystal structure of E.coli RppH-DapF complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.06 Å

Oligo State

hetero-2-2-mer

Ligands

20 x IOD: IODIDE ION(Non-functional Binders)

IOD.1: 5 residues within 4Å: Chain A: F.14, G.77, A.78, R.79, C.80 Ligand excluded by PLIP IOD.2: 4 residues within 4Å: Chain A: N.12, R.79, A.217, G.219 Ligand excluded by PLIP IOD.3: 2 residues within 4Å: Chain A: F.26, S.27 Ligand excluded by PLIP IOD.4: 3 residues within 4Å: Chain A: R.83, R.86, D.113 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: R.143, R.185 Ligand excluded by PLIP IOD.6: 1 residues within 4Å: Chain A: A.172 Ligand excluded by PLIP IOD.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain A: H.38 Chain C: R.37 Ligands: IOD.21 Ligand excluded by PLIP IOD.11: 1 residues within 4Å: Chain A: P.51 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain B: K.82, R.83 Ligand excluded by PLIP IOD.14: 5 residues within 4Å: Chain C: F.14, G.77, A.78, R.79, C.80 Ligand excluded by PLIP IOD.15: 4 residues within 4Å: Chain C: N.12, R.79, A.217, G.219 Ligand excluded by PLIP IOD.16: 2 residues within 4Å: Chain C: F.26, S.27 Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain C: R.83, R.86, D.113 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain C: R.143, R.185 Ligand excluded by PLIP IOD.19: 1 residues within 4Å: Chain C: A.172 Ligand excluded by PLIP IOD.20: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain A: R.37 Chain C: H.38 Ligands: IOD.8 Ligand excluded by PLIP IOD.24: 1 residues within 4Å: Chain C: P.51 Ligand excluded by PLIP IOD.25: 2 residues within 4Å: Chain D: K.82, R.83 Ligand excluded by PLIP

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

CL.9: 4 residues within 4Å: Chain A: L.57, R.97, R.104, M.105 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: V.106 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: C.93, Q.96 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain C: L.57, R.97, R.104, M.105 Ligand excluded by PLIP CL.23: 1 residues within 4Å: Chain C: V.106 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain D: C.93, Q.96 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, A. et al., Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF. Nucleic Acids Res. (2018)

Release Date

2018-05-23

Peptides

Diaminopimelate epimerase: AC
RNA pyrophosphohydrolase: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Diaminopimelate epimerase

RNA pyrophosphohydrolase

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