SMTL ID : 5b8f.1

X-ray Crystal Structure of a 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Pseudomonas aeruginosa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-trimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.15, H.17, H.49 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.15, A:H.17, A:H.49 MG.4: 3 residues within 4Å: Chain B: D.15, H.17, H.49 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.15, B:H.17, B:H.49, H2O.15 MG.10: 3 residues within 4Å: Chain C: D.15, H.17, H.49 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.15, C:H.17, C:H.49

3 x C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

C5P.2: 11 residues within 4Å: Chain A: A.107, P.110, K.111, M.112, A.113, A.138, T.139, T.140, E.142 Chain B: D.63, G.65 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.138, A:T.140 Hydrogen bonds: A:A.107, A:M.112, A:A.113, A:A.138, A:T.140, A:T.140, A:E.142, B:D.63 Water bridges: A:T.140, A:E.142, B:D.63, B:G.65 pi-Cation interactions: A:K.111 C5P.5: 9 residues within 4Å: Chain B: A.107, P.110, K.111, M.112, A.113, A.138, T.139, T.140 Chain C: D.63 16 PLIP interactions: 10 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:A.138, B:T.140 Hydrogen bonds: B:A.107, B:M.112, B:A.113, B:T.139, B:T.140 Water bridges: B:A.138, B:T.140, B:E.142, C:D.15, C:D.63, C:D.63, C:D.63, C:D.63, C:G.65 C5P.11: 12 residues within 4Å: Chain A: D.63, G.65, K.66 Chain C: A.107, P.110, K.111, M.112, A.113, A.138, T.139, T.140, E.142 15 PLIP interactions: 11 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:A.138, C:T.140 Hydrogen bonds: C:A.107, C:M.112, C:A.113, C:A.138, C:T.139, C:T.140, C:E.142, A:D.63 Water bridges: C:T.139, C:T.140, A:K.66, A:K.66, A:K.66

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 5 residues within 4Å: Chain A: F.68, R.74, A.78, A.82, L.83 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.68, A:L.83 Water bridges: A:R.74

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

PO4.6: 9 residues within 4Å: Chain A: G.145, F.146, R.149 Chain B: G.145, F.146, R.149 Chain C: G.145, R.149 Ligands: PO4.9 11 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A, 4 interactions with chain C Hydrogen bonds: B:F.146, A:G.145, A:F.146, C:G.145 Water bridges: B:R.149, B:E.151, C:F.146, C:F.146 Salt bridges: B:R.149, A:R.149, C:R.149 PO4.7: 6 residues within 4Å: Chain A: Y.14, H.156 Chain B: Y.14, H.156 Chain C: Y.14, H.156 9 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C, 3 interactions with chain B Water bridges: A:Y.14, C:Y.14, C:Y.14, C:Y.14, B:Y.14, B:Y.14 Salt bridges: A:H.156, C:H.156, B:H.156 PO4.8: 1 residues within 4Å: Chain B: R.164 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.97, B:R.164 PO4.9: 4 residues within 4Å: Chain A: R.149 Chain B: R.149 Chain C: R.149 Ligands: PO4.6 7 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B, 2 interactions with chain A Water bridges: C:R.149, C:R.149, B:R.149, A:R.149 Salt bridges: C:R.149, B:R.149, A:R.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

SSGCID et al., X-ray Crystal Structure of a 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Pseudomonas aeruginosa. to be published

Release Date

2015-05-06

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

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