SMTL ID : 6vpq.2 (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

5 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: W.182, P.183, E.184 Ligands: PGE.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.184 MG.2: 2 residues within 4Å: Chain A: D.187, I.190 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.187, A:I.190, H2O.3 MG.3: 3 residues within 4Å: Chain A: A.149, Q.150, S.153 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:Q.150, A:S.153 MG.4: 3 residues within 4Å: Chain A: K.142, Q.145, R.146 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain A: I.175, D.176, Q.179, D.187 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.176, H2O.1, H2O.2

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

PGE.6: 6 residues within 4Å: Chain A: I.139, D.140, E.143, K.181, W.182 Ligands: MG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.138, A:D.140 PGE.7: 6 residues within 4Å: Chain A: P.121, K.124, G.155, A.156, S.157, Q.167 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.156, A:S.157, A:Q.167 Water bridges: A:K.124, A:K.124

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 1 residues within 4Å: Chain A: E.180 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.180

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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