SMTL ID : 7l4a.1

Crystal Structure of Cytidylate kinase from Encephalitozoon cuniculi GB-M1 in complex with two CDP molecules

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

2 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)

CDP.1: 19 residues within 4Å: Chain A: A.13, K.17, S.35, G.36, Y.39, R.40, R.88, V.96, A.100, R.106, G.128, R.129, D.130, I.131, R.156, R.175, D.179, R.182 Ligands: CDP.2 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:Y.39 Hydrogen bonds: A:A.14, A:S.35, A:R.106, A:R.106, A:R.129, A:R.129, A:D.130, A:D.130, A:R.156, A:R.175, A:R.175, A:D.179, A:R.182, A:R.182 Water bridges: A:Y.39, A:R.40, A:R.88, A:R.88, A:R.88, A:D.127, A:D.179 Salt bridges: A:K.17, A:R.40, A:R.40, A:R.88, A:R.129, A:R.129, A:R.175 CDP.2: 14 residues within 4Å: Chain A: A.14, S.15, G.16, K.17, S.18, S.19, R.155, R.156, E.159, N.198, M.201, T.202, L.203 Ligands: CDP.1 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:A.14, A:S.15, A:G.16, A:K.17, A:S.18, A:S.19, A:S.19, A:R.156, A:E.159, A:M.201 Water bridges: A:S.18, A:S.18, A:R.88, A:R.155, A:R.155, A:R.155, A:R.155, A:N.198 Salt bridges: A:K.17, A:R.156 pi-Cation interactions: A:R.155

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

SO4.3: 3 residues within 4Å: Chain A: E.90, V.91, R.94 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.90, A:V.91 Salt bridges: A:R.94

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

EDO.4: 5 residues within 4Å: Chain A: K.103, R.106, E.107, F.110, D.185 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J.A. et al., Crystal Structure of Cytidylate kinase from Encephalitozoon cuniculi GB-M1 in complex with two CDP molecules. to be published

Release Date

2020-12-30

Peptides

Cytidylate kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytidylate kinase