SMTL ID : 5e5g.1

3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with D-tryptophan bound in the tryptophan and phenylalanine binding sites

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

10 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.285 Water bridges: A:E.250, A:K.308, A:R.339 Salt bridges: A:K.308, A:R.339, A:H.371 SO4.5: 5 residues within 4Å: Chain B: G.284, E.285, K.308, R.339, H.371 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:E.285 Water bridges: B:R.286, B:R.286, B:K.308, B:K.308, B:K.308, B:R.339 Salt bridges: B:K.308, B:R.339, B:H.371 SO4.6: 3 residues within 4Å: Chain B: R.25, L.28, R.258 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.258 Water bridges: B:R.51 Salt bridges: B:R.25, B:R.258 SO4.7: 4 residues within 4Å: Chain B: R.137, S.138, A.139, R.286 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.138, B:S.138, B:A.139 Salt bridges: B:R.137, B:R.286 SO4.8: 3 residues within 4Å: Chain B: P.19, L.20, R.25 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.20 Salt bridges: B:R.25 SO4.12: 5 residues within 4Å: Chain C: G.284, E.285, K.308, R.339, H.371 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:E.285 Water bridges: C:E.250, C:K.308, C:R.339 Salt bridges: C:K.308, C:R.339, C:H.371 SO4.16: 5 residues within 4Å: Chain D: G.284, E.285, K.308, R.339, H.371 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:E.285 Water bridges: D:R.286, D:R.286, D:K.308, D:K.308, D:K.308, D:R.339 Salt bridges: D:K.308, D:R.339, D:H.371 SO4.17: 3 residues within 4Å: Chain D: R.25, L.28, R.258 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.55, D:R.258 Water bridges: D:R.51 Salt bridges: D:R.25, D:R.258 SO4.18: 4 residues within 4Å: Chain D: R.137, S.138, A.139, R.286 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.138, D:S.138, D:A.139 Salt bridges: D:R.137, D:R.286 SO4.19: 3 residues within 4Å: Chain D: P.19, L.20, R.25 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.20 Salt bridges: D:R.25

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

MN.2: 4 residues within 4Å: Chain A: C.89, H.371, 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.7 MN.9: 4 residues within 4Å: Chain B: C.89, H.371, E.413, D.443 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.89, B:H.371, B:E.413, B:D.443, H2O.18 MN.13: 4 residues within 4Å: Chain C: C.89, H.371, 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.32 MN.20: 4 residues within 4Å: Chain D: C.89, H.371, E.413, D.443 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.89, D:H.371, D:E.413, D:D.443, H2O.43

8 x DTR: D-TRYPTOPHAN(Non-covalent)

DTR.3: 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 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:W.5, B:V.57, B:Y.175, B:Y.175, B:A.176, A:A.176 Water bridges: B:D.8, B:S.179 Hydrogen bonds: A:F.93, A:A.176, A:N.177, A:N.177 Salt bridges: A:R.173 DTR.4: 11 residues within 4Å: Chain A: L.109, A.112, V.113, K.125, A.194, L.196, N.239, L.240, T.242, A.243 Chain C: C.233 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.109, A:A.112, A:V.113, A:L.196 Hydrogen bonds: A:A.194, A:N.239 Water bridges: A:V.123 Salt bridges: A:K.125 DTR.10: 9 residues within 4Å: Chain A: V.53, V.172, Y.175 Chain B: W.5, F.93, R.173, A.176, N.177, A.180 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.5, B:A.176, B:A.180 Hydrogen bonds: B:W.5, B:F.93, B:N.177 Water bridges: B:R.173 Salt bridges: B:R.173 pi-Stacking: A:Y.175 DTR.11: 10 residues within 4Å: Chain B: L.109, V.113, K.125, A.194, L.196, N.239, L.240, T.242, A.243 Chain D: C.233 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.109, B:V.113, B:L.196 Hydrogen bonds: B:A.194, B:N.239 Water bridges: B:V.123 Salt bridges: B:K.125 DTR.14: 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 13 PLIP interactions: 6 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:W.5, D:V.57, D:Y.175, D:Y.175, D:A.176, C:A.176 Water bridges: D:S.179, C:R.173 Hydrogen bonds: C:F.93, C:A.176, C:N.177, C:N.177 Salt bridges: C:R.173 DTR.15: 11 residues within 4Å: Chain A: C.233 Chain C: L.109, A.112, V.113, K.125, A.194, L.196, N.239, L.240, T.242, A.243 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.109, C:A.112, C:V.113, C:L.196 Hydrogen bonds: C:A.194, C:N.239 Water bridges: C:V.123 Salt bridges: C:K.125 DTR.21: 9 residues within 4Å: Chain C: V.53, V.172, Y.175 Chain D: W.5, F.93, R.173, A.176, N.177, A.180 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:W.5, D:A.176, D:A.180 Hydrogen bonds: D:W.5, D:F.93, D:N.177 Water bridges: D:R.173 Salt bridges: D:R.173 pi-Stacking: C:Y.175 DTR.22: 10 residues within 4Å: Chain B: C.233 Chain D: L.109, V.113, K.125, A.194, L.196, N.239, L.240, T.242, A.243 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.109, D:V.113, D:L.196 Hydrogen bonds: D:A.194, D:N.239 Water bridges: D:V.123 Salt bridges: D:K.125

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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