SMTL ID : 3t80.2 (1 other biounit)

Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium bound to cytidine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.11, H.13, H.45 Ligands: MG.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.11, A:D.11, A:H.13, A:H.45, H2O.1 ZN.7: 4 residues within 4Å: Chain B: D.11, H.13, H.45 Ligands: MG.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.11, B:D.11, B:H.13, B:H.45 ZN.12: 6 residues within 4Å: Chain B: E.138 Chain C: D.11, V.12, H.13, H.45 Ligands: MG.13 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.11, C:D.11, C:H.13

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.11 Chain C: T.135 Ligands: ZN.1 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:D.11, C:T.135, H2O.1, H2O.1 MG.3: 3 residues within 4Å: Chain A: E.152 Chain B: E.152 Chain C: E.152 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 2 interactions with chain B Metal complexes: A:E.152, C:E.152, C:E.152, B:E.152, B:E.152 MG.8: 3 residues within 4Å: Chain A: T.135 Chain B: D.11 Ligands: ZN.7 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.11, A:T.135, H2O.1 MG.13: 3 residues within 4Å: Chain B: T.135 Chain C: D.11 Ligands: ZN.12 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Metal complexes: B:T.135, C:D.11

3 x CTN: 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE(Non-covalent)

CTN.4: 12 residues within 4Å: Chain A: A.103, Q.104, P.106, K.107, M.108, L.109, A.134, T.135, T.136 Chain B: D.59, G.61, K.62 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.134, A:T.136 Hydrogen bonds: A:P.106, A:M.108, A:L.109, A:A.134, B:G.61 CTN.9: 9 residues within 4Å: Chain B: A.103, P.106, K.107, M.108, L.109, A.134, T.135, T.136 Chain C: D.59 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:T.136 Hydrogen bonds: B:A.103, B:M.108, B:L.109 Water bridges: B:A.134 CTN.14: 12 residues within 4Å: Chain A: D.59, G.61, K.62, D.66 Chain C: A.103, P.106, K.107, M.108, L.109, A.134, T.135, T.136 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:A.134, C:T.136 Hydrogen bonds: C:P.106, C:M.108, C:L.109, C:A.134, A:G.61, A:G.61 Water bridges: C:T.135, C:T.136

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

EDO.5: 3 residues within 4Å: Chain A: F.142, T.143 Ligands: POP.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.143 EDO.6: 2 residues within 4Å: Chain A: L.140 Chain B: E.147 No protein-ligand interaction detected (PLIP) EDO.11: 4 residues within 4Å: Chain B: F.142, T.143, A.150 Ligands: POP.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.142 EDO.15: 4 residues within 4Å: Chain C: I.102, F.142, T.143 Ligands: POP.10 No protein-ligand interaction detected (PLIP) EDO.16: 2 residues within 4Å: Chain B: K.139, L.140 No protein-ligand interaction detected (PLIP)

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.10: 12 residues within 4Å: Chain A: G.141, F.142, R.145 Chain B: G.141, F.142, R.145 Chain C: G.141, F.142, R.145 Ligands: EDO.5, EDO.11, EDO.15 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:F.142, C:F.142, A:F.142 Salt bridges: B:R.145, C:R.145, A:R.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seattle Structural Genomics Center for Infectious Disease (SSGCID) et al., Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium bound to cytidine. To be Published

Release Date

2011-09-14

Peptides

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Related Entries With Identical Sequence