SMTL ID : 5e4n.1

3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis with D-tyrosine bound in the tyrosine and phenylalanine binding sites

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: G.284, E.285, K.308, R.339, H.371 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.285 Water bridges: A:R.286, A:R.286, A:K.308, A:K.308, A:R.339, A:R.339 Salt bridges: A:K.308, A:R.339, A:H.371 SO4.6: 5 residues within 4Å: Chain B: G.284, E.285, K.308, R.339, H.371 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.285 Water bridges: B:R.286, B:R.286, B:K.308 Salt bridges: B:K.308, B:R.339, B:H.371 SO4.7: 5 residues within 4Å: Chain B: P.136, R.137, S.138, A.139, R.286 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:P.136, B:S.138, B:A.139 Water bridges: B:R.286, B:R.286 Salt bridges: B:R.137, B:R.286 SO4.8: 5 residues within 4Å: Chain B: P.18, P.19, L.20, R.25 Ligands: DTY.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.20 Salt bridges: B:R.25 SO4.14: 5 residues within 4Å: Chain C: G.284, E.285, K.308, R.339, H.371 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:E.285 Water bridges: C:R.286, C:R.286, C:K.308, C:K.308, C:R.339, C:R.339 Salt bridges: C:K.308, C:R.339, C:H.371 SO4.19: 5 residues within 4Å: Chain D: G.284, E.285, K.308, R.339, H.371 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.285 Water bridges: D:R.286, D:R.286, D:K.308 Salt bridges: D:K.308, D:R.339, D:H.371 SO4.20: 5 residues within 4Å: Chain D: P.136, R.137, S.138, A.139, R.286 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:P.136, D:S.138, D:A.139 Water bridges: D:R.286, D:R.286 Salt bridges: D:R.137, D:R.286 SO4.21: 5 residues within 4Å: Chain D: P.18, P.19, L.20, R.25 Ligands: DTY.26 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.20 Salt bridges: D:R.25

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: R.137, D.142, A.143 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: R.51, R.258 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: V.62, P.63, S.64 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain B: R.102 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain C: R.137, D.142, A.143 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain C: R.51, R.258 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain D: V.62, P.63, S.64 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Chain D: R.102 Ligand excluded by PLIP

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 5 residues within 4Å: Chain A: C.89, H.371, R.384, E.413, D.443 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.89, A:H.371, A:E.413, A:D.443, H2O.5 MN.10: 4 residues within 4Å: Chain B: C.89, H.371, E.413, D.443 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:C.89, B:H.371, B:E.413, B:E.413, B:D.443 MN.16: 5 residues within 4Å: Chain C: C.89, H.371, R.384, E.413, D.443 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.89, C:H.371, C:E.413, C:D.443, H2O.25 MN.23: 4 residues within 4Å: Chain D: C.89, H.371, E.413, D.443 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:C.89, D:H.371, D:E.413, D:E.413, D:D.443

6 x DTY: D-TYROSINE(Non-covalent)

DTY.5: 9 residues within 4Å: Chain A: F.93, R.173, A.176, N.177 Chain B: W.5, V.57, V.172, Y.175, A.176 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:F.93, A:F.93, A:N.177 Water bridges: A:R.173 Salt bridges: A:R.173 Hydrophobic interactions: B:W.5, B:V.57, B:V.172, B:Y.175 DTY.12: 10 residues within 4Å: Chain A: D.12, L.14, V.57, V.172, Y.175, A.176 Chain B: F.93, R.173, A.176, N.177 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.57, A:V.172, A:Y.175 Water bridges: A:A.176, B:A.176 Hydrogen bonds: B:F.93, B:N.177, B:N.177 Salt bridges: B:R.173 DTY.13: 9 residues within 4Å: Chain B: P.18, L.20, R.25, L.28, R.51, E.55, R.258, L.261 Ligands: SO4.8 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.20, B:L.20, B:L.20, B:L.28, B:L.261 Hydrogen bonds: B:P.18, B:R.51, B:E.55, B:E.55 Water bridges: B:L.261 Salt bridges: B:R.25, B:R.258 DTY.18: 9 residues within 4Å: Chain C: F.93, R.173, A.176, N.177 Chain D: W.5, V.57, V.172, Y.175, A.176 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:F.93, C:F.93, C:N.177 Water bridges: C:R.173 Salt bridges: C:R.173 Hydrophobic interactions: D:W.5, D:V.57, D:V.172, D:Y.175 DTY.25: 10 residues within 4Å: Chain C: D.12, L.14, V.57, V.172, Y.175, A.176 Chain D: F.93, R.173, A.176, N.177 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:F.93, D:N.177, D:N.177 Water bridges: D:A.176, C:A.176 Salt bridges: D:R.173 Hydrophobic interactions: C:V.57, C:V.172, C:Y.175 DTY.26: 9 residues within 4Å: Chain D: P.18, L.20, R.25, L.28, R.51, E.55, R.258, L.261 Ligands: SO4.21 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:L.20, D:L.20, D:L.20, D:L.28, D:L.261 Hydrogen bonds: D:P.18, D:R.51, D:E.55 Water bridges: D:L.261 Salt bridges: D:R.25, D:R.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reichau, S. et al., Probing the Sophisticated Synergistic Allosteric Regulation of Aromatic Amino Acid Biosynthesis in Mycobacterium tuberculosis Using -Amino Acids. Plos One (2016)

Release Date

2016-06-01

Peptides

3-deoxy-D-arabinoheptulosonate-7-phosphate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

3-deoxy-D-arabinoheptulosonate-7-phosphate synthase

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