SMTL ID : 5qpb.1

PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with FMOPL000701a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

monomer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: A.49, F.53, D.59, K.61 No protein-ligand interaction detected (PLIP) EDO.2: 4 residues within 4Å: Chain A: P.129, N.130, K.131 Ligands: ACT.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.129, 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: S.29, R.102 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.29, A:R.102 Water bridges: A:L.26 ACT.5: 5 residues within 4Å: Chain A: R.116, P.129, N.130, F.133 Ligands: EDO.2 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 PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 11 residues within 4Å: Chain A: V.22, Q.23, G.24, K.28, G.30, W.31, G.32, K.35, G.36, E.55, M.134 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.24, A:K.28, A:K.28

1 x LJA: N-[3-(carbamoylamino)phenyl]acetamide(Non-covalent)

LJA.7: 8 residues within 4Å: Chain A: T.6, K.35, I.74, Q.77, A.79, F.133, M.134, F.138 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.6, A:I.74, A:I.74, A:Q.77, A:F.138 Hydrogen bonds: A:T.6, A:K.35, A:N.75

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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