SMTL ID : 5qp4.1

PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with Z450133538

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

monomer

Ligands

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: A.49, R.50, F.53, D.59, K.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.59 Water bridges: A:R.50 EDO.2: 4 residues within 4Å: Chain A: P.129, N.130, K.131 Ligands: ACT.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.129, A:N.130, A:K.131

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 4 residues within 4Å: Chain A: N.18, W.106, F.107, S.108 No protein-ligand interaction detected (PLIP)

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

ACT.4: 2 residues within 4Å: Chain A: L.26, S.29 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.29 Water bridges: A:L.26, A:R.102, A:R.102 ACT.5: 6 residues within 4Å: Chain A: R.116, P.129, N.130, F.133 Ligands: EDO.2, LH7.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.133 Hydrogen bonds: A:N.130 Salt bridges: A:R.116

1 x LH7: 1-[(3S)-1,1-dioxo-1lambda~6~-thiolan-3-yl]-N-[(4-fluorophenyl)methyl]-5-methyl-1H-pyrazole-4-carboxamide(Non-covalent)

LH7.6: 13 residues within 4Å: Chain A: V.22, G.24, A.27, K.28, G.32, F.33, K.35, E.55, E.100, I.101, F.133, M.134 Ligands: ACT.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.22, A:K.28, A:K.28, A:I.101 Hydrogen bonds: A:K.28, A:G.30 Halogen bonds: A:E.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nelson, E.R. et al., PanDDA analysis group deposition. To Be Published

Release Date

2019-05-08

Peptides

DCP2 (NUDT20): A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DCP2 (NUDT20)

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