SMTL ID : 7oqx.1

Crystal structure of a psychrophilic CCA-adding enzyme in complex with CMPcPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x 2TM: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine(Non-covalent)

2TM.1: 14 residues within 4Å: Chain A: G.65, G.66, R.69, H.78, R.150, D.151, N.155, D.193, R.196, R.199, R.202, F.203, Q.206, K.240 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.66, A:R.69, A:H.78, A:R.150, A:D.151, A:N.155, A:R.196, A:R.196, A:R.199, A:R.199, A:R.202, A:R.202, A:Q.206, A:R.233, A:K.240 Water bridges: A:R.150 Salt bridges: A:R.69, A:R.202 pi-Cation interactions: A:R.199

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

PO4.2: 7 residues within 4Å: Chain A: R.311, K.315, K.332, Y.333, T.334, Q.337 Ligands: ACT.11 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.332, A:T.334, A:Q.337, A:Q.337, A:Q.337 Salt bridges: A:R.311, A:K.315 PO4.3: 2 residues within 4Å: Chain A: T.298, K.301 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.298, A:T.298, A:T.298 Salt bridges: A:K.301

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

ACT.4: 1 residues within 4Å: Chain A: R.343 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.343 ACT.5: 3 residues within 4Å: Chain A: D.326, Y.398, I.400 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.398 ACT.6: 5 residues within 4Å: Chain A: E.308, L.312, T.334, K.336, Q.337 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.334 Hydrogen bonds: A:Q.337, A:Q.337 Salt bridges: A:K.336 ACT.7: 2 residues within 4Å: Chain A: K.92, D.100 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.100 Salt bridges: A:K.92 ACT.8: 3 residues within 4Å: Chain A: M.213, K.214, L.217 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.214, A:L.217 Water bridges: A:K.214 ACT.9: 3 residues within 4Å: Chain A: R.311, K.315 Ligands: ACT.11 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.311, A:K.315 ACT.10: 3 residues within 4Å: Chain A: Q.248, Y.276, H.277 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.278 Salt bridges: A:H.277 ACT.11: 7 residues within 4Å: Chain A: R.311, K.315, E.318, K.332, Y.333 Ligands: PO4.2, ACT.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.332 Salt bridges: A:K.315 ACT.12: 1 residues within 4Å: Chain A: K.255 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.255

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 3 residues within 4Å: Chain A: L.71, G.74, K.75 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Wijn, R. et al., CCA-addition in the cold: Structural characterization of the psychrophilic CCA-adding enzyme from the permafrost bacterium Planococcus halocryophilus . Comput Struct Biotechnol J (2021)

Release Date

2021-11-03

Peptides

CCA-adding enzyme: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CCA-adding enzyme

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