SMTL ID : 5ex4.1

3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis complexed with tryptophan in all three allosteric binding sites

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 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.6 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.18: 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.33 MN.26: 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.46

10 x TRP: TRYPTOPHAN(Non-covalent)

TRP.2: 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: A.232, C.233 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:L.109, A:V.113, A:L.196 Hydrogen bonds: A:A.194, A:N.239, C:A.232 Water bridges: A:K.125, A:K.125, A:N.239, A:N.239 Salt bridges: A:K.125 TRP.4: 11 residues within 4Å: Chain A: F.93, M.94, R.173, A.176, N.177, A.180 Chain B: I.9, V.53, V.57, Y.175 Ligands: GOL.7 9 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:A.176, A:A.180, B:V.57 Hydrogen bonds: A:F.93, A:N.177, A:N.177, W.4 Salt bridges: A:R.173 pi-Stacking: B:Y.175 TRP.10: 12 residues within 4Å: Chain A: I.11, D.12, Q.13, V.172, Y.175, A.176 Chain B: F.93, R.173, A.176, N.177, A.180 Ligands: GOL.7 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:A.176, B:A.180 Hydrogen bonds: B:F.93, B:N.177, A:D.12 Salt bridges: B:R.173 pi-Stacking: A:Y.175 TRP.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 12 PLIP interactions: 9 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: B:V.113, B:L.196 Hydrogen bonds: B:A.194, B:N.239, W.11, W.11 Water bridges: B:K.125, B:N.239, B:N.239, B:N.239, W.11 Salt bridges: B:K.125 TRP.15: 12 residues within 4Å: Chain B: L.17, P.18, L.20, R.25, L.28, E.55, R.258, L.261, R.262, L.263, L.273 Ligands: CL.16 15 PLIP interactions: 13 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:L.20, B:L.20, B:L.28, B:L.261, B:L.273 Hydrogen bonds: B:P.18, B:E.55, B:R.258, W.15 Water bridges: B:R.51, B:R.258, B:L.261, W.15 Salt bridges: B:R.25, B:R.258 TRP.19: 12 residues within 4Å: Chain A: A.232, C.233 Chain C: L.109, A.112, V.113, K.125, A.194, L.196, N.239, L.240, T.242, A.243 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: C:L.109, C:V.113, C:L.196 Hydrogen bonds: C:A.194, C:N.239, A:A.232 Water bridges: C:K.125, C:K.125, C:N.239, C:N.239 Salt bridges: C:K.125 TRP.21: 11 residues within 4Å: Chain C: F.93, M.94, R.173, A.176, N.177, A.180 Chain D: I.9, V.53, V.57, Y.175 Ligands: GOL.24 9 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: C:A.176, C:A.180, D:V.57 Hydrogen bonds: C:F.93, C:N.177, C:N.177, W.21 Salt bridges: C:R.173 pi-Stacking: D:Y.175 TRP.27: 12 residues within 4Å: Chain C: I.11, D.12, Q.13, V.172, Y.175, A.176 Chain D: F.93, R.173, A.176, N.177, A.180 Ligands: GOL.24 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C, Hydrophobic interactions: D:A.176, D:A.180 Hydrogen bonds: D:F.93, D:N.177, C:D.12 Salt bridges: D:R.173 pi-Stacking: C:Y.175 TRP.28: 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 12 PLIP interactions: 9 interactions with chain D, 3 Ligand-Ligand interactions Hydrophobic interactions: D:V.113, D:L.196 Hydrogen bonds: D:A.194, D:N.239, W.28, W.28 Water bridges: D:T.116, D:N.239, D:N.239, D:N.239, W.28 Salt bridges: D:K.125 TRP.32: 12 residues within 4Å: Chain D: L.17, P.18, L.20, R.25, L.28, E.55, R.258, L.261, R.262, L.263, L.273 Ligands: CL.33 16 PLIP interactions: 14 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:L.20, D:L.20, D:L.28, D:L.261, D:L.273 Hydrogen bonds: D:P.18, D:E.55, D:E.55, D:R.258, W.32 Water bridges: D:R.51, D:R.258, D:L.261, W.32 Salt bridges: D:R.25, D:R.258

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

SO4.3: 5 residues within 4Å: Chain A: T.41, D.140, R.147, R.150, H.166 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.140 Salt bridges: A:R.147, A:R.150, A:H.166 SO4.8: 4 residues within 4Å: Chain B: R.137, S.138, A.139, R.286 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.138, B:A.139 Salt bridges: B:R.137, B:R.286 SO4.20: 5 residues within 4Å: Chain C: T.41, D.140, R.147, R.150, H.166 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.140 Salt bridges: C:R.147, C:R.150, C:H.166 SO4.25: 4 residues within 4Å: Chain D: R.137, S.138, A.139, R.286 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.138, D:A.139 Salt bridges: D:R.137, D:R.286

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: E.65, M.182, R.186, T.189, A.243, E.244, I.245, H.279 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.189, A:I.245 Water bridges: A:E.65, A:T.189, A:T.189, A:E.244 GOL.7: 8 residues within 4Å: Chain A: I.9, P.10, I.11, V.172 Chain B: V.7, I.9 Ligands: TRP.4, TRP.10 3 PLIP interactions: 2 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: W.4, W.10, A:P.10 GOL.12: 3 residues within 4Å: Chain B: R.27, Q.299, V.300 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.27, B:Q.299, B:Q.299 GOL.13: 9 residues within 4Å: Chain B: E.65, R.68, M.182, T.189, A.243, E.244, I.245, Y.246, H.279 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.65, B:R.68, B:R.68, B:T.189, B:T.189, B:I.245 Water bridges: B:E.65 GOL.17: 5 residues within 4Å: Chain B: Q.72, P.122, V.123, V.124, E.244 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.72, B:V.123 Water bridges: B:K.125, B:K.125, B:K.125, B:N.239 GOL.22: 8 residues within 4Å: Chain C: E.65, M.182, R.186, T.189, A.243, E.244, I.245, H.279 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.189, C:T.189, C:I.245 Water bridges: C:E.65, C:E.65, C:E.244 GOL.24: 8 residues within 4Å: Chain C: I.9, P.10, I.11, V.172 Chain D: V.7, I.9 Ligands: TRP.21, TRP.27 3 PLIP interactions: 2 Ligand-Ligand interactions, 1 interactions with chain C Hydrogen bonds: W.21, W.27, C:P.10 GOL.29: 3 residues within 4Å: Chain D: R.27, Q.299, V.300 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.27, D:Q.299, D:Q.299 GOL.30: 9 residues within 4Å: Chain D: E.65, R.68, M.182, T.189, A.243, E.244, I.245, Y.246, H.279 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.65, D:R.68, D:R.68, D:T.189, D:I.245 Water bridges: D:T.189, D:T.189 GOL.34: 5 residues within 4Å: Chain D: Q.72, P.122, V.123, V.124, E.244 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Q.72, D:V.123, D:E.244 Water bridges: D:K.125, D:K.125, D:K.125, D:N.239

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

PO4.6: 5 residues within 4Å: Chain A: G.284, E.285, K.308, R.339, H.371 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.285 Water bridges: A:E.250, A:R.286, A:K.308, A:K.308 Salt bridges: A:K.308, A:R.339, A:H.371 PO4.14: 5 residues within 4Å: Chain B: G.284, E.285, K.308, R.339, H.371 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.285 Water bridges: B:R.286, B:R.286, B:R.286, B:R.286, B:K.308 Salt bridges: B:K.308, B:R.339, B:H.371 PO4.23: 5 residues within 4Å: Chain C: G.284, E.285, K.308, R.339, H.371 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:E.285 Water bridges: C:E.250, C:R.286, C:K.308, C:K.308 Salt bridges: C:K.308, C:R.339, C:H.371 PO4.31: 5 residues within 4Å: Chain D: G.284, E.285, K.308, R.339, H.371 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:E.285 Water bridges: D:R.286, D:R.286, D:R.286, D:R.286, D:K.308 Salt bridges: D:K.308, D:R.339, D:H.371

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

CL.16: 4 residues within 4Å: Chain B: P.19, L.20, R.25 Ligands: TRP.15 Ligand excluded by PLIP CL.33: 4 residues within 4Å: Chain D: P.19, L.20, R.25 Ligands: TRP.32 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reichau, S. et al., 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis complexed with tryptophan in all three allosteric binding sites. to be published

Release Date

2015-12-02

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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