SMTL ID : 3hl4.1

Crystal structure of a mammalian CTP:phosphocholine cytidylyltransferase with CDP-choline

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x CDC: [2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM(Non-covalent)

CDC.1: 20 residues within 4Å: Chain A: D.82, G.83, I.84, F.85, H.89, G.91, H.92, A.95, C.113, K.122, P.150, W.151, H.168, D.169, Y.173, Y.182, Q.195, R.196, T.197, I.200 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:I.84, A:F.85, A:H.168, A:D.169, A:D.169, A:R.196, A:T.197, A:T.197 Water bridges: A:D.86, A:R.196, A:T.197 Salt bridges: A:D.82, A:H.92, A:K.122, A:K.122, A:H.168 pi-Cation interactions: A:W.151, A:W.151, A:Y.173, A:R.196 CDC.7: 21 residues within 4Å: Chain B: D.82, G.83, I.84, F.85, H.89, G.91, H.92, A.95, C.113, K.122, P.150, W.151, H.168, D.169, Y.173, V.181, Y.182, Q.195, R.196, T.197, I.200 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:I.84, B:F.85, B:H.168, B:D.169, B:Y.173, B:R.196, B:T.197, B:T.197 Water bridges: B:D.86, B:T.194, B:R.196 Salt bridges: B:D.82, B:H.92, B:K.122, B:K.122, B:H.168 pi-Cation interactions: B:W.151, B:Y.173, B:R.196

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: D.170, K.186, F.191, P.193 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.170, A:K.186

7 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 4 residues within 4Å: Chain A: E.198, G.199, I.200 Chain B: E.131 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.131 Water bridges: B:N.128 FMT.4: 2 residues within 4Å: Chain A: I.171, R.196 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.196 Water bridges: A:Q.195 FMT.5: 3 residues within 4Å: Chain A: R.42, Q.43 Chain B: N.101 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.42, A:R.42, A:Q.43 FMT.6: 1 residues within 4Å: Chain A: E.198 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.198 FMT.8: 2 residues within 4Å: Chain B: S.178, D.179 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.179, B:D.179 FMT.9: 6 residues within 4Å: Chain B: F.47, S.48, D.49, V.145, V.146, R.147 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.49, B:R.147, B:R.147 FMT.10: 3 residues within 4Å: Chain B: N.128, E.129, N.130 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.130, B:N.130 Water bridges: B:D.115, B:D.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, J. et al., Crystal Structure of a mammalian CTP: Phosphocholine cytidylyltransferase catalytic domain reveals novel active site residues within a highly conserved nucleotidyl-transferase fold. J.Biol.Chem. (2009)

Release Date

2009-09-22

Peptides

Choline-phosphate cytidylyltransferase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Choline-phosphate cytidylyltransferase A