SMTL ID : 6vpq.6 (5 other biounits)

Crystal structure of the C-terminal domain of DENR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

monomer

Ligands

7 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.191 Ligands: MG.3, MG.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.191, A:E.191, H2O.1, H2O.2, H2O.3 MG.2: 3 residues within 4Å: Chain A: P.121, R.122, K.124 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:R.122 MG.3: 4 residues within 4Å: Chain A: D.187, I.190, E.191 Ligands: MG.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.187, A:I.190, H2O.1, H2O.1, H2O.3 MG.4: 3 residues within 4Å: Chain A: D.188, E.191 Ligands: MG.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.188, A:E.191, H2O.1, H2O.3 MG.5: 1 residues within 4Å: Chain A: E.195 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.195 MG.6: 4 residues within 4Å: Chain A: T.171, D.172, E.195 Ligands: MG.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.171, A:D.172, A:E.195, H2O.1 MG.7: 4 residues within 4Å: Chain A: T.171, D.192, E.195 Ligands: MG.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.192, A:E.195

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.8: 2 residues within 4Å: Chain A: D.187 Ligands: ACT.11 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.179 PGE.9: 5 residues within 4Å: Chain A: F.137, E.138, I.139, W.182, E.184 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.184 Water bridges: A:E.138, A:E.143

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 5 residues within 4Å: Chain A: K.124, K.125, C.154, G.155, Q.167 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.124, A:Q.167 Hydrogen bonds: A:G.155 Salt bridges: A:K.125 ACT.11: 3 residues within 4Å: Chain A: Q.179, D.187 Ligands: PGE.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.187 Water bridges: A:Q.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lomakin, I.B. et al., Crystal structure of the C-terminal domain of DENR. Comput Struct Biotechnol J (2020)

Release Date

2020-04-08

Peptides

Density-regulated protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

Density-regulated protein

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