SMTL ID : 5e2l.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 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 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 SO4.8: 4 residues within 4Å: Chain B: R.25, L.28, R.51, R.258 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.51, B:R.258 Salt bridges: B:R.25, B:R.258 SO4.9: 5 residues within 4Å: Chain B: G.284, E.285, K.308, R.339, H.371 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.285 Salt bridges: B:K.308, B:R.339, B:H.371 SO4.10: 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 SO4.11: 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 SO4.17: 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 SO4.24: 4 residues within 4Å: Chain D: R.25, L.28, R.51, R.258 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.51, D:E.55, D:R.258 Salt bridges: D:R.25, D:R.258 SO4.25: 5 residues within 4Å: Chain D: G.284, E.285, K.308, R.339, H.371 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.285 Salt bridges: D:K.308, D:R.339, D:H.371 SO4.26: 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 SO4.27: 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

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: 5 interactions with chain A Metal complexes: A:C.89, A:H.371, A:E.413, A:E.413, A:D.443 MN.12: 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.18: 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.28: 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

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

CL.3: 3 residues within 4Å: Chain A: R.137, D.142, A.143 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: V.62, P.63, S.64 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: Q.38 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: P.63, S.64 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain B: Q.38 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain C: R.137, D.142, A.143 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain C: V.62, P.63, S.64 Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain C: Q.38 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain D: P.63, S.64 Ligand excluded by PLIP CL.31: 1 residues within 4Å: Chain D: Q.38 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: Q.72, P.122, V.123, V.124, E.244 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.72, A:V.123, A:E.244, A:E.244 Water bridges: A:K.125, A:K.125 GOL.14: 5 residues within 4Å: Chain B: Q.72, V.123, V.124, K.125, E.244 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.125, B:E.244 Water bridges: B:V.123, B:K.125 GOL.20: 5 residues within 4Å: Chain C: Q.72, P.122, V.123, V.124, E.244 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.72, C:V.123, C:E.244 Water bridges: C:K.125, C:K.125 GOL.30: 5 residues within 4Å: Chain D: Q.72, V.123, V.124, K.125, E.244 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.125, D:E.244, D:E.244 Water bridges: D:V.123, D:K.125

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

DPN.7: 9 residues within 4Å: Chain A: F.93, M.94, R.173, A.176, N.177 Chain B: W.5, V.7, V.57, Y.175 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:W.5, B:V.57, B:Y.175, A:A.176 Hydrogen bonds: A:F.93, A:N.177, A:N.177 Salt bridges: A:R.173 DPN.16: 7 residues within 4Å: Chain A: V.57, V.172, Y.175 Chain B: F.93, R.173, A.176, N.177 7 PLIP interactions: 4 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 Salt bridges: B:R.173 DPN.23: 9 residues within 4Å: Chain C: F.93, M.94, R.173, A.176, N.177 Chain D: W.5, V.7, V.57, Y.175 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:W.5, D:V.57, D:Y.175, C:A.176 Hydrogen bonds: C:F.93, C:N.177, C:N.177 Salt bridges: C:R.173 DPN.32: 7 residues within 4Å: Chain C: V.57, V.172, Y.175 Chain D: F.93, R.173, A.176, N.177 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:A.176, C:V.57, C:V.172, C:Y.175 Hydrogen bonds: D:F.93, D:N.177 Salt bridges: D:R.173

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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