SMTL ID : 3aua.1

Crystal structure of the quaternary complex-2 of an isomerase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 26 residues within 4Å: Chain A: G.84, T.86, G.87, S.88, I.89, Y.113, V.114, N.115, K.116, S.117, H.136, G.180, I.181, D.182, S.183, Q.185, A.203, N.204, K.205, E.206, D.231, M.298, G.299, I.302, M.360 Ligands: F98.3 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:I.89, A:I.302 Hydrogen bonds: A:G.84, A:T.86, A:T.86, A:T.86, A:S.88, A:S.88, A:S.88, A:I.89, A:N.115, A:K.116, A:S.117, A:S.117, A:H.136, A:I.181, A:D.182, A:D.182, A:S.183, A:N.204, A:K.205, A:G.299 Water bridges: A:G.87, A:G.90, A:N.115, A:N.115, A:K.300, A:K.300, A:K.301 pi-Stacking: A:Y.113 NDP.4: 27 residues within 4Å: Chain B: G.84, S.85, T.86, G.87, S.88, I.89, Y.113, V.114, N.115, K.116, S.117, H.136, G.180, I.181, D.182, S.183, Q.185, A.203, N.204, K.205, E.206, D.231, M.298, G.299, I.302, M.360 Ligands: F98.6 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:I.89, B:I.302 Hydrogen bonds: B:G.84, B:T.86, B:T.86, B:T.86, B:G.87, B:S.88, B:S.88, B:S.88, B:I.89, B:N.115, B:K.116, B:S.117, B:S.117, B:H.136, B:I.181, B:D.182, B:S.183, B:Q.185, B:N.204, B:K.205, B:E.206, B:G.299 Water bridges: B:G.90, B:N.115, B:N.115, B:K.300, B:K.300, B:K.300 pi-Stacking: B:Y.113

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: K.205, D.231, S.232, E.233, E.315 Ligands: F98.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.231, A:E.233, A:E.233, A:E.315 MG.5: 6 residues within 4Å: Chain B: K.205, D.231, S.232, E.233, E.315 Ligands: F98.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.231, B:E.233, B:E.233, B:E.315

2 x F98: 3-[ethanoyl(hydroxy)amino]propylphosphonic acid(Non-covalent)

F98.3: 19 residues within 4Å: Chain A: K.205, D.231, S.232, E.233, S.269, S.270, G.271, G.272, H.293, W.296, M.298, I.302, S.306, N.311, K.312, E.315, M.360 Ligands: NDP.1, MG.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.296 Hydrogen bonds: A:K.205, A:D.231, A:S.232, A:S.270, A:G.271, A:G.272, A:H.293, A:N.311, A:K.312 Water bridges: A:E.233, A:S.269, A:S.269, A:K.312 F98.6: 19 residues within 4Å: Chain B: K.205, D.231, S.232, E.233, S.269, S.270, G.271, G.272, H.293, W.296, M.298, I.302, S.306, N.311, K.312, E.315, M.360 Ligands: NDP.4, MG.5 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:W.296 Hydrogen bonds: B:K.205, B:D.231, B:S.232, B:S.270, B:G.271, B:G.272, B:H.293, B:N.311, B:K.312, B:K.312 Water bridges: B:S.269, B:S.269, B:S.269, B:S.269

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 2 residues within 4Å: Chain B: S.139, E.143 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.139, B:E.143, B:E.143, H2O.12, H2O.15 CA.8: 3 residues within 4Å: Chain A: D.242 Chain B: Q.239, L.241 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:Q.239, B:L.241, A:D.242, H2O.10, H2O.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Umeda, T. et al., Molecular basis of fosmidomycin's action on the human malaria parasite Plasmodium falciparum. Sci Rep (2011)

Release Date

2011-08-10

Peptides

1-deoxy-D-xylulose 5-phosphate reductoisomerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

1-deoxy-D-xylulose 5-phosphate reductoisomerase

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