SMTL ID : 2ypq.1

3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with tryptophan and tyrosine bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.76 Å

Oligo State

homo-tetramer

Ligands

6 x TYR: TYROSINE(Non-covalent)

TYR.1: 9 residues within 4Å: Chain A: F.91, N.94, R.171, A.174, N.175 Chain B: V.5, V.55, Y.173, A.174 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B, Hydrogen bonds: A:F.91, A:N.175 Salt bridges: A:R.171 Hydrophobic interactions: B:V.55, B:Y.173 TYR.9: 8 residues within 4Å: Chain A: D.10, V.55, Y.173, A.174 Chain B: F.91, R.171, A.174, N.175 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A, Hydrogen bonds: B:F.91, B:A.174, B:N.175, A:D.10 Salt bridges: B:R.171 Hydrophobic interactions: A:V.55, A:Y.173 TYR.10: 7 residues within 4Å: Chain B: P.16, L.18, R.23, L.26, E.53, R.256, L.261 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:L.18, B:L.26 Hydrogen bonds: B:P.16, B:E.53, B:E.53 Salt bridges: B:R.23, B:R.49, B:R.256 TYR.18: 9 residues within 4Å: Chain C: F.91, N.94, R.171, A.174, N.175 Chain D: V.5, V.55, Y.173, A.174 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D, Hydrogen bonds: C:F.91, C:N.175 Salt bridges: C:R.171 Hydrophobic interactions: D:V.55, D:Y.173 TYR.26: 8 residues within 4Å: Chain C: D.10, V.55, Y.173, A.174 Chain D: F.91, R.171, A.174, N.175 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:V.55, C:Y.173 Hydrogen bonds: C:D.10, D:F.91, D:A.174, D:N.175 Salt bridges: D:R.171 TYR.27: 7 residues within 4Å: Chain D: P.16, L.18, R.23, L.26, E.53, R.256, L.261 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.18, D:L.26 Hydrogen bonds: D:P.16, D:E.53 Salt bridges: D:R.23, D:R.49, D:R.256

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

MN.2: 4 residues within 4Å: Chain A: C.87, H.369, E.411, D.441 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.87, A:H.369, A:E.411, A:D.441 MN.11: 5 residues within 4Å: Chain B: C.87, R.126, H.369, E.411, D.441 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.87, B:H.369, B:E.411, B:D.441 MN.19: 4 residues within 4Å: Chain C: C.87, H.369, E.411, D.441 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.87, C:H.369, C:E.411, C:D.441 MN.28: 5 residues within 4Å: Chain D: C.87, R.126, H.369, E.411, D.441 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.87, D:H.369, D:E.411, D:D.441

4 x TRP: TRYPTOPHAN(Non-covalent)

TRP.3: 11 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 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:A.110, A:L.194 Hydrogen bonds: A:A.192, A:N.237, C:C.231 Salt bridges: A:K.123 TRP.12: 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.16 9 PLIP interactions: 8 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:L.107, B:V.111, B:V.111, B:L.194 Hydrogen bonds: B:A.192, B:L.194, B:N.237 Salt bridges: B:K.123 Water bridges: W.12 TRP.20: 11 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 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: C:A.110, C:L.194 Hydrogen bonds: C:A.192, C:N.237, C:N.237, A:C.231 Salt bridges: C:K.123 TRP.29: 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.33 9 PLIP interactions: 1 Ligand-Ligand interactions, 8 interactions with chain D Water bridges: W.29 Hydrophobic interactions: D:L.107, D:V.111, D:V.111, D:L.194 Hydrogen bonds: D:A.192, D:L.194, D:N.237 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.283 Salt bridges: A:K.306, A:R.337, A:H.369 PO4.13: 5 residues within 4Å: Chain B: G.282, E.283, K.306, R.337, H.369 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.283 Salt bridges: B:K.306, B:R.337, B:H.369 PO4.21: 5 residues within 4Å: Chain C: G.282, E.283, K.306, R.337, H.369 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.283 Salt bridges: C:K.306, C:R.337, C:H.369 PO4.30: 5 residues within 4Å: Chain D: G.282, E.283, K.306, R.337, H.369 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.283 Salt bridges: D:K.306, D:R.337, D:H.369

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

SO4.5: 5 residues within 4Å: Chain A: T.39, D.138, R.145, R.148, H.164 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.145 Salt bridges: A:R.145, A:H.164 SO4.14: 4 residues within 4Å: Chain B: P.134, R.135, S.136, A.137 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.136, B:A.137, B:A.137 Salt bridges: B:R.135, B:R.284 SO4.22: 5 residues within 4Å: Chain C: T.39, D.138, R.145, R.148, H.164 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.145 Salt bridges: C:R.145, C:H.164 SO4.31: 4 residues within 4Å: Chain D: P.134, R.135, S.136, A.137 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.136, D:A.137, D:A.137 Salt bridges: D:R.135, D:R.284

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

CL.6: 2 residues within 4Å: Chain A: R.223, R.226 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: Q.36 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain C: R.223, R.226 Ligand excluded by PLIP CL.25: 1 residues within 4Å: Chain C: Q.36 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: E.63, M.180, R.184, T.187, E.242, I.243, Y.244, H.277 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.187, A:A.241, A:I.243 GOL.15: 7 residues within 4Å: Chain A: S.188 Chain B: E.63, R.184, T.187, E.242, I.243, H.277 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.188, B:T.187, B:I.243, B:I.243 Water bridges: B:T.187 GOL.16: 7 residues within 4Å: Chain B: Q.70, P.120, V.121, V.122, K.123, E.242 Ligands: TRP.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.121, B:K.123, B:K.123, B:E.242, B:E.242 GOL.17: 6 residues within 4Å: Chain B: L.30, A.34, Q.37, L.252, D.253, R.256 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.256 GOL.24: 8 residues within 4Å: Chain C: E.63, M.180, R.184, T.187, E.242, I.243, Y.244, H.277 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.241, C:I.243 Water bridges: C:T.187, C:T.187 GOL.32: 7 residues within 4Å: Chain C: S.188 Chain D: E.63, R.184, T.187, E.242, I.243, H.277 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:E.63, D:T.187, D:T.187, D:I.243, D:I.243, C:S.188 GOL.33: 7 residues within 4Å: Chain D: Q.70, P.120, V.121, V.122, K.123, E.242 Ligands: TRP.29 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:V.121, D:K.123, D:K.123, D:E.242 GOL.34: 6 residues within 4Å: Chain D: L.30, A.34, Q.37, L.252, D.253, R.256 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blackmore, N.J. et al., Three Sites and You are Out: Ternary Synergistic Allostery Controls Aromatic Aminoacid Biosynthesis in Mycobacterium Tuberculosis. J.Mol.Biol. (2013)

Release Date

2013-01-09

Peptides

PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE AROG: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE AROG

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