SMTL ID : 1jyl.1

Catalytic Mechanism of CTP:phosphocholine Cytidylyltransferase from Streptococcus pneumoniae (LicC)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.127, E.236, D.238 Ligands: CDC.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.127, A:E.236, A:D.238 MG.3: 5 residues within 4Å: Chain B: K.48, D.127, E.236, D.238 Ligands: CDC.4 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.127, B:D.127, B:E.236, B:D.238, H2O.4 MG.5: 4 residues within 4Å: Chain C: D.127, E.236, D.238 Ligands: CDC.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.127, C:E.236, C:D.238 MG.7: 5 residues within 4Å: Chain D: K.48, D.127, E.236, D.238 Ligands: CDC.8 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.127, D:D.127, D:E.236, D:D.238, H2O.7

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

CDC.2: 18 residues within 4Å: Chain A: L.31, A.32, A.33, G.34, Y.102, Y.105, N.106, N.107, S.110, D.125, A.126, D.127, W.156, Y.210, D.212, E.236, D.238 Ligands: MG.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:N.107 Hydrogen bonds: A:A.32, A:A.33, A:G.34, A:Y.105, A:N.107, A:S.110, A:A.126, A:D.127, A:D.127, A:Y.210 Salt bridges: A:D.212 pi-Cation interactions: A:W.156, A:W.156, A:Y.210 CDC.4: 21 residues within 4Å: Chain A: P.41, E.44 Chain B: L.31, A.32, A.33, G.34, K.48, Y.102, Y.105, N.106, N.107, S.110, D.125, A.126, D.127, W.156, Y.210, D.212, E.236, D.238 Ligands: MG.3 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:A.32, B:A.33, B:G.34, B:N.99, B:Y.105, B:N.107, B:S.110, B:D.127, B:D.127 Salt bridges: B:K.48, B:D.212 pi-Cation interactions: B:W.156, B:W.156, B:Y.210 CDC.6: 18 residues within 4Å: Chain C: L.31, A.32, A.33, G.34, Y.102, Y.105, N.106, N.107, S.110, D.125, A.126, D.127, W.156, Y.210, D.212, E.236, D.238 Ligands: MG.5 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:N.107 Hydrogen bonds: C:A.33, C:G.34, C:K.48, C:N.99, C:Y.105, C:N.107, C:S.110, C:A.126, C:D.127, C:Y.210 Salt bridges: C:D.212 pi-Cation interactions: C:W.156, C:W.156, C:Y.210 CDC.8: 21 residues within 4Å: Chain C: P.41, E.44 Chain D: L.31, A.32, A.33, G.34, K.48, Y.102, Y.105, N.106, N.107, S.110, D.125, A.126, D.127, W.156, Y.210, D.212, E.236, D.238 Ligands: MG.7 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:N.107 Hydrogen bonds: D:A.33, D:G.34, D:Y.105, D:N.107, D:S.110, D:A.126, D:D.127, D:D.127 Salt bridges: D:K.48, D:D.212 pi-Cation interactions: D:W.156, D:W.156, D:Y.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwak, B.Y. et al., Structure and mechanism of CTP:phosphocholine cytidylyltransferase (LicC) from Streptococcus pneumoniae. J.Biol.Chem. (2002)

Release Date

2002-02-22

Peptides

CTP:phosphocholine Cytidylyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

CTP:phosphocholine Cytidylyltransferase

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