SMTL ID : 3rzi.1

The structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis cocrystallized and complexed with phenylalanine and tryptophan

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: C.87, H.369, R.382, E.411, D.441 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.87, A:H.369, A:E.411, A:D.441, H2O.4 MN.10: 4 residues within 4Å: Chain B: C.87, H.369, E.411, D.441 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.87, B:H.369, B:E.411, B:D.441, H2O.12 MN.23: 5 residues within 4Å: Chain C: C.87, H.369, R.382, E.411, D.441 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.87, C:H.369, C:E.411, C:D.441, H2O.23 MN.32: 4 residues within 4Å: Chain D: C.87, H.369, E.411, D.441 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.87, D:H.369, D:E.411, D:D.441, H2O.31

4 x PHE: PHENYLALANINE(Non-covalent)

PHE.2: 10 residues within 4Å: Chain A: F.91, M.92, R.171, A.174, N.175, A.178 Chain B: V.5, D.6, V.55, Y.173 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A, Hydrophobic interactions: B:Y.173, A:A.174, A:A.178 Hydrogen bonds: B:D.6, A:F.91, A:N.175 Salt bridges: A:R.171 PHE.12: 7 residues within 4Å: Chain A: V.55, Y.173 Chain B: F.91, R.171, A.174, N.175, A.178 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.174, B:A.178, A:V.55, A:Y.173 Hydrogen bonds: B:F.91, B:N.175 Salt bridges: B:R.171 PHE.24: 10 residues within 4Å: Chain C: F.91, M.92, R.171, A.174, N.175, A.178 Chain D: V.5, D.6, V.55, Y.173 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D, Hydrophobic interactions: C:A.174, C:A.178, D:Y.173 Hydrogen bonds: C:F.91, C:N.175, D:D.6 Salt bridges: C:R.171 PHE.34: 7 residues within 4Å: Chain C: V.55, Y.173 Chain D: F.91, R.171, A.174, N.175, A.178 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain D, Hydrophobic interactions: C:V.55, C:Y.173, D:A.174, D:A.178 Hydrogen bonds: D:F.91, D:N.175 Salt bridges: D:R.171

4 x TRP: TRYPTOPHAN(Non-covalent)

TRP.3: 12 residues within 4Å: Chain A: L.107, A.110, V.111, K.123, A.192, L.194, N.237, L.238, T.240, A.241 Chain C: C.231 Ligands: GOL.7 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:A.110, A:V.111 Hydrogen bonds: A:A.192, A:N.237 Water bridges: A:K.123, A:K.123 Salt bridges: A:K.123 TRP.13: 12 residues within 4Å: Chain B: L.107, A.110, V.111, K.123, A.192, L.194, N.237, L.238, T.240, A.241 Chain D: C.231 Ligands: GOL.22 12 PLIP interactions: 1 Ligand-Ligand interactions, 10 interactions with chain B, 1 interactions with chain D Water bridges: W.13, B:K.123, B:K.123, B:K.123, B:N.237, D:A.230 Hydrophobic interactions: B:L.107, B:A.110, B:V.111 Hydrogen bonds: B:A.192, B:N.237 Salt bridges: B:K.123 TRP.25: 12 residues within 4Å: Chain A: C.231 Chain C: L.107, A.110, V.111, K.123, A.192, L.194, N.237, L.238, T.240, A.241 Ligands: GOL.29 7 PLIP interactions: 7 interactions with chain C, Hydrophobic interactions: C:A.110, C:V.111 Hydrogen bonds: C:A.192, C:N.237 Water bridges: C:K.123, C:K.123 Salt bridges: C:K.123 TRP.35: 12 residues within 4Å: Chain B: C.231 Chain D: L.107, A.110, V.111, K.123, A.192, L.194, N.237, L.238, T.240, A.241 Ligands: GOL.44 12 PLIP interactions: 10 interactions with chain D, 1 Ligand-Ligand interactions, 1 interactions with chain B Hydrophobic interactions: D:L.107, D:A.110, D:V.111 Hydrogen bonds: D:A.192, D:N.237 Water bridges: D:K.123, D:K.123, D:K.123, D:N.237, W.35, B:A.230 Salt bridges: D:K.123

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

PO4.4: 5 residues within 4Å: Chain A: G.282, E.283, K.306, R.337, H.369 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.283 Water bridges: A:R.284, A:R.284, A:K.306, A:K.306 Salt bridges: A:K.306, A:R.337, A:H.369 PO4.14: 6 residues within 4Å: Chain B: G.282, E.283, R.284, K.306, R.337, H.369 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:E.283, B:R.284 Water bridges: B:K.306, B:K.306, B:K.306, B:R.337, B:R.337 Salt bridges: B:K.306, B:R.337, B:H.369 PO4.26: 5 residues within 4Å: Chain C: G.282, E.283, K.306, R.337, H.369 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:E.283 Water bridges: C:R.284, C:R.284, C:K.306, C:K.306 Salt bridges: C:K.306, C:R.337, C:H.369 PO4.36: 6 residues within 4Å: Chain D: G.282, E.283, R.284, K.306, R.337, H.369 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:E.283, D:R.284 Water bridges: D:K.306, D:K.306, D:K.306, D:R.337, D:R.337 Salt bridges: D:K.306, D:R.337, D:H.369

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

SO4.5: 4 residues within 4Å: Chain A: T.39, R.145, R.148, H.164 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.145, A:R.148, A:H.164 SO4.15: 4 residues within 4Å: Chain B: R.135, S.136, A.137, R.284 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.136, B:S.136, B:A.137 Water bridges: B:R.284, B:R.284 Salt bridges: B:R.135, B:R.284 SO4.16: 3 residues within 4Å: Chain B: P.17, L.18, R.23 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.18 Water bridges: B:L.18 Salt bridges: B:R.23 SO4.17: 3 residues within 4Å: Chain B: R.23, L.26, R.256 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.49, B:R.49 Salt bridges: B:R.23, B:R.256 SO4.27: 4 residues within 4Å: Chain C: T.39, R.145, R.148, H.164 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:R.145, C:R.148, C:H.164 SO4.37: 4 residues within 4Å: Chain D: R.135, S.136, A.137, R.284 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.136, D:S.136, D:A.137 Water bridges: D:R.284, D:R.284 Salt bridges: D:R.135, D:R.284 SO4.38: 3 residues within 4Å: Chain D: P.17, L.18, R.23 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.18 Water bridges: D:L.18 Salt bridges: D:R.23 SO4.39: 3 residues within 4Å: Chain D: R.23, L.26, R.256 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.53 Water bridges: D:R.49, D:R.49 Salt bridges: D:R.23, D:R.256

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: E.63, R.184, T.187, A.241, E.242, I.243, Y.244 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain A: Q.70, P.120, V.121, V.122, K.123, E.242 Ligands: TRP.3 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: R.135, S.136, A.137, R.284, K.380 Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain B: L.30, A.34, D.253, R.256 Ligand excluded by PLIP GOL.19: 2 residues within 4Å: Chain B: Q.297, R.322 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain B: M.180, R.184, T.187, A.241, E.242, I.243, H.277 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain B: M.92, D.93, F.155, E.437 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain B: Q.70, P.120, V.121, V.122, E.242 Ligands: TRP.13 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain C: E.63, R.184, T.187, A.241, E.242, I.243, Y.244 Ligand excluded by PLIP GOL.29: 7 residues within 4Å: Chain C: Q.70, P.120, V.121, V.122, K.123, E.242 Ligands: TRP.25 Ligand excluded by PLIP GOL.31: 5 residues within 4Å: Chain C: R.135, S.136, A.137, R.284, K.380 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain D: L.30, A.34, D.253, R.256 Ligand excluded by PLIP GOL.41: 2 residues within 4Å: Chain D: Q.297, R.322 Ligand excluded by PLIP GOL.42: 7 residues within 4Å: Chain D: M.180, R.184, T.187, A.241, E.242, I.243, H.277 Ligand excluded by PLIP GOL.43: 4 residues within 4Å: Chain D: M.92, D.93, F.155, E.437 Ligand excluded by PLIP GOL.44: 6 residues within 4Å: Chain D: Q.70, P.120, V.121, V.122, E.242 Ligands: TRP.35 Ligand excluded by PLIP

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

CL.8: 1 residues within 4Å: Chain A: Q.36 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain B: R.49, R.256 Ligand excluded by PLIP CL.30: 1 residues within 4Å: Chain C: Q.36 Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain D: R.49, R.256 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiao, W. et al., Dynamic cross-talk among remote binding sites: the molecular basis for unusual synergistic allostery. J.Mol.Biol. (2012)

Release Date

2012-01-25

Peptides

Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG

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