SMTL ID : 5e7z.1

3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis in complex with D/L-tryptophan and D-phenylalanine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: D.140, R.147, R.150, H.166 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.41 Salt bridges: A:R.147, A:R.150, A:H.166 SO4.2: 5 residues within 4Å: Chain A: G.284, E.285, K.308, R.339, H.371 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.285 Water bridges: A:K.308 Salt bridges: A:K.308, A:R.339, A:H.371 SO4.7: 6 residues within 4Å: Chain B: G.284, E.285, R.286, K.308, R.339, H.371 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.285, B:R.286 Salt bridges: B:K.308, B:R.339, B:H.371 SO4.8: 4 residues within 4Å: Chain B: R.25, L.28, E.55, R.258 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.51 Salt bridges: B:R.25, B:R.258 SO4.14: 4 residues within 4Å: Chain C: D.140, R.147, R.150, H.166 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.41 Salt bridges: C:R.147, C:R.150, C:H.166 SO4.15: 5 residues within 4Å: Chain C: G.284, E.285, K.308, R.339, H.371 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.285 Water bridges: C:K.308 Salt bridges: C:K.308, C:R.339, C:H.371 SO4.20: 6 residues within 4Å: Chain D: G.284, E.285, R.286, K.308, R.339, H.371 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.285, D:R.286 Salt bridges: D:K.308, D:R.339, D:H.371 SO4.21: 4 residues within 4Å: Chain D: R.25, L.28, E.55, R.258 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.51 Salt bridges: D:R.25, D:R.258

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

MN.3: 4 residues within 4Å: Chain A: C.89, H.371, E.413, D.443 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.89, A:H.371, A:E.413, A:E.413, A:D.443 MN.9: 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: 4 residues within 4Å: Chain C: C.89, H.371, E.413, D.443 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:C.89, C:H.371, C:E.413, C:E.413, C:D.443 MN.22: 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

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

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 Chain C: C.233 Ligands: TRP.5 12 PLIP interactions: 7 interactions with chain A, 1 interactions with chain C, 4 Ligand-Ligand interactions Hydrophobic interactions: A:L.109, A:A.112, W.5, W.5, W.5 Hydrogen bonds: A:A.194, A:N.239, C:A.232 Water bridges: A:V.123, A:N.239, W.5 Salt bridges: A:K.125 DTR.11: 12 residues within 4Å: Chain B: L.109, A.112, V.113, K.125, A.194, L.196, N.239, L.240, T.242, A.243 Chain D: C.233 Ligands: TRP.12 11 PLIP interactions: 6 interactions with chain B, 5 Ligand-Ligand interactions Hydrophobic interactions: B:L.109, B:A.112, B:V.113, W.12, W.12, W.12, W.12 Hydrogen bonds: B:A.194, B:N.239 Salt bridges: B:K.125 pi-Stacking: W.12 DTR.17: 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 Ligands: TRP.18 12 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A, 4 Ligand-Ligand interactions Hydrophobic interactions: C:L.109, C:A.112, W.18, W.18, W.18 Hydrogen bonds: C:A.194, C:N.239, A:A.232 Water bridges: C:V.123, C:N.239, W.18 Salt bridges: C:K.125 DTR.24: 12 residues within 4Å: Chain B: C.233 Chain D: L.109, A.112, V.113, K.125, A.194, L.196, N.239, L.240, T.242, A.243 Ligands: TRP.25 11 PLIP interactions: 6 interactions with chain D, 5 Ligand-Ligand interactions Hydrophobic interactions: D:L.109, D:A.112, D:V.113, W.25, W.25, W.25, W.25 Hydrogen bonds: D:A.194, D:N.239 Salt bridges: D:K.125 pi-Stacking: W.25

4 x TRP: TRYPTOPHAN(Non-covalent)

TRP.5: 12 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 Ligands: DTR.4 9 PLIP interactions: 7 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:L.109, A:A.112 Hydrogen bonds: A:A.194, A:N.239, W.5, W.5 Water bridges: A:N.239, A:N.239 Salt bridges: A:K.125 TRP.12: 12 residues within 4Å: Chain B: L.109, A.112, V.113, K.125, A.194, L.196, N.239, L.240, T.242, A.243 Chain D: C.233 Ligands: DTR.11 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:L.109, B:A.112 Hydrogen bonds: B:A.194, B:N.239 Salt bridges: B:K.125 TRP.18: 12 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 Ligands: DTR.17 9 PLIP interactions: 7 interactions with chain C, 2 Ligand-Ligand interactions Hydrophobic interactions: C:L.109, C:A.112 Hydrogen bonds: C:A.194, C:N.239, W.18, W.18 Water bridges: C:N.239, C:N.239 Salt bridges: C:K.125 TRP.25: 12 residues within 4Å: Chain B: C.233 Chain D: L.109, A.112, V.113, K.125, A.194, L.196, N.239, L.240, T.242, A.243 Ligands: DTR.24 5 PLIP interactions: 5 interactions with chain D, Hydrophobic interactions: D:L.109, D:A.112 Hydrogen bonds: D:A.194, D:N.239 Salt bridges: D:K.125

4 x DPN: D-PHENYLALANINE(Non-covalent)

DPN.6: 8 residues within 4Å: Chain A: F.93, R.173, A.176, N.177 Chain B: W.5, V.7, V.57, Y.175 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:W.5, B:V.7, B:V.57, B:Y.175, A:A.176 Hydrogen bonds: A:F.93, A:F.93, A:N.177 Water bridges: A:R.173 Salt bridges: A:R.173 DPN.13: 8 residues within 4Å: Chain A: V.57, V.172, Y.175, A.176 Chain B: F.93, R.173, A.176, N.177 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.176, A:V.57, A:V.172, A:Y.175 Hydrogen bonds: B:F.93, B:N.177, B:N.177 Salt bridges: B:R.173 DPN.19: 8 residues within 4Å: Chain C: F.93, R.173, A.176, N.177 Chain D: W.5, V.7, V.57, Y.175 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:A.176, D:W.5, D:V.7, D:V.57, D:Y.175 Hydrogen bonds: C:F.93, C:F.93, C:N.177 Salt bridges: C:R.173 Water bridges: D:D.8 DPN.26: 8 residues within 4Å: Chain C: V.57, V.172, Y.175, A.176 Chain D: F.93, R.173, A.176, N.177 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:V.57, C:V.172, C:Y.175, D:A.176 Hydrogen bonds: D:F.93, D:N.177, D:N.177 Salt bridges: D:R.173

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 8 residues within 4Å: Chain B: E.65, R.186, T.189, A.243, E.244, I.245, Y.246, H.279 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.189, B:I.245, B:H.279 Water bridges: B:E.65, A:S.190, A:S.190 GOL.23: 8 residues within 4Å: Chain D: E.65, R.186, T.189, A.243, E.244, I.245, Y.246, H.279 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:T.189, D:T.189, D:I.245, D:H.279 Water bridges: D:E.65, C:S.190, C:S.190

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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