SMTL ID : 6vpr.2 (1 other biounit)

Crystal structure of the C-terminal domain of DENR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

2 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.1: 4 residues within 4Å: Chain A: R.130, L.193, G.194, E.195 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.130, A:L.193 Water bridges: A:R.130 Salt bridges: A:R.130 TLA.2: 2 residues within 4Å: Chain A: K.125, Y.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.125 Salt bridges: A:K.125, A:K.125

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 2 residues within 4Å: Chain A: Q.145, R.146 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.145 Salt bridges: A:R.146

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 3 residues within 4Å: Chain A: G.168, D.169 Ligands: HG.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.169, A:D.169 Salt bridges: A:K.126

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

ACT.5: 3 residues within 4Å: Chain A: C.154, G.155 Ligands: HG.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.155 ACT.6: 3 residues within 4Å: Chain A: R.130, C.132 Ligands: HG.7 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.130 Salt bridges: A:R.130

2 x HG: MERCURY (II) ION(Non-covalent)

HG.7: 3 residues within 4Å: Chain A: C.132, E.163 Ligands: ACT.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.132 HG.8: 4 residues within 4Å: Chain A: C.154, Q.167 Ligands: SO4.4, ACT.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.154

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
B

Density-regulated protein

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