SMTL ID : 3mio.1 (1 other biounit)

Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase domain from Mycobacterium tuberculosis at pH 6.00

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 3 residues within 4Å: Chain A: D.5, S.6, R.9 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.5, A:D.5, A:D.5, A:S.6, A:S.6 Water bridges: A:R.3 PO4.2: 5 residues within 4Å: Chain A: R.141, G.143, H.144, T.145 Ligands: GOL.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:H.144, A:T.145, A:T.145, A:T.145 Water bridges: A:D.33, A:H.144, A:H.144, A:E.165, A:E.165 Salt bridges: A:R.141, A:H.144 PO4.6: 3 residues within 4Å: Chain B: D.5, S.6, R.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.5, B:D.5, B:S.6, B:S.6 Water bridges: B:R.3 PO4.7: 5 residues within 4Å: Chain B: R.141, G.143, H.144, T.145 Ligands: GOL.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.144, B:T.145, B:T.145 Water bridges: B:D.33, B:H.144, B:T.145 Salt bridges: B:R.141, B:H.144

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: Y.56, L.131 Chain B: H.127 Ligands: PO4.2 No protein-ligand interaction detected (PLIP) GOL.4: 2 residues within 4Å: Chain A: E.39, K.40 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.39, A:K.40 Water bridges: A:E.39, A:K.40, A:Q.158 GOL.8: 4 residues within 4Å: Chain A: H.127 Chain B: Y.56, L.131 Ligands: PO4.7 No protein-ligand interaction detected (PLIP) GOL.9: 2 residues within 4Å: Chain B: E.39, K.40 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.40 Water bridges: B:E.39, B:K.40, B:Q.158

2 x K: POTASSIUM ION(Non-covalent)

K.5: 5 residues within 4Å: Chain A: V.50, R.51, T.53 Chain B: V.50 Ligands: K.10 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:V.50, A:R.51, A:T.53, B:V.50, H2O.14 K.10: 5 residues within 4Å: Chain A: V.50 Chain B: V.50, R.51, T.53 Ligands: K.5 5 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:V.50, B:V.50, B:R.51, B:T.53, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, M. et al., Structural basis for pH dependent monomer-dimer transition of 3,4-dihydroxy 2-butanone-4-phosphate synthase domain from Mycobacterium tuberculosis. J.Struct.Biol. (2011)

Release Date

2011-02-23

Peptides

3,4-dihydroxy-2-butanone 4-phosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3,4-dihydroxy-2-butanone 4-phosphate synthase

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