SMTL ID : 2ypp.1

3-deoxy-D-arabino-heptulosonate 7-phosphate synthase in complex with 3 tyrosine molecules

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

6 x TYR: TYROSINE(Non-covalent)

TYR.1: 9 residues within 4Å: Chain A: F.91, R.171, A.174, N.175 Chain B: W.3, V.5, V.55, Y.173, A.174 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A, Hydrophobic interactions: B:W.3, B:V.55, B:Y.173 Hydrogen bonds: B:D.6, A:F.91, A:N.175 Water bridges: B:A.174, A:A.174 Salt bridges: A:R.171 TYR.10: 8 residues within 4Å: Chain A: I.9, V.55, Y.173, A.174 Chain B: F.91, R.171, A.174, N.175 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A, Hydrogen bonds: B:F.91, B:A.174, B:N.175 Salt bridges: B:R.171 Hydrophobic interactions: A:V.55, A:Y.173 TYR.11: 8 residues within 4Å: Chain B: L.15, P.16, L.18, R.23, L.26, E.53, R.256, L.259 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.15, B:L.18, B:L.18, B:L.18, B:L.26, B:L.259 Hydrogen bonds: B:P.16, B:E.53 Water bridges: B:L.259 Salt bridges: B:R.23, B:R.256 TYR.18: 9 residues within 4Å: Chain C: F.91, R.171, A.174, N.175 Chain D: W.3, V.5, V.55, Y.173, A.174 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain D, Hydrogen bonds: C:F.91, C:N.175, D:D.6 Water bridges: C:A.174, D:A.174 Salt bridges: C:R.171 Hydrophobic interactions: D:W.3, D:V.55, D:Y.173 TYR.27: 8 residues within 4Å: Chain C: I.9, V.55, Y.173, A.174 Chain D: F.91, R.171, A.174, N.175 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:F.91, D:A.174, D:N.175 Salt bridges: D:R.171 Hydrophobic interactions: C:V.55, C:Y.173 TYR.28: 8 residues within 4Å: Chain D: L.15, P.16, L.18, R.23, L.26, E.53, R.256, L.259 12 PLIP interactions: 12 interactions with chain D, Hydrophobic interactions: D:L.15, D:L.18, D:L.18, D:L.18, D:L.26, D:L.259 Hydrogen bonds: D:P.16, D:E.53, D:E.53 Water bridges: D:L.259 Salt bridges: D:R.23, 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 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.87, A:H.369, A:E.411, A:E.411, A:D.441 MN.9: 4 residues within 4Å: Chain B: C.87, H.369, E.411, D.441 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:C.87, B:H.369, B:E.411, B:E.411, B:D.441 MN.19: 4 residues within 4Å: Chain C: C.87, H.369, E.411, D.441 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:C.87, C:H.369, C:E.411, C:E.411, C:D.441 MN.26: 4 residues within 4Å: Chain D: C.87, H.369, E.411, D.441 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:C.87, D:H.369, D:E.411, D:E.411, D:D.441

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

SO4.3: 5 residues within 4Å: Chain A: G.282, E.283, K.306, R.337, H.369 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.283 Water bridges: A:W.280 Salt bridges: A:K.306, A:R.337, A:H.369 SO4.4: 4 residues within 4Å: Chain A: R.135, S.136, A.137, R.284 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.136, A:A.137, A:A.137 Salt bridges: A:R.135, A:R.284 SO4.7: 2 residues within 4Å: Chain A: A.35, Q.36 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.36, A:Q.36 Water bridges: A:Q.37, A:Q.37 SO4.12: 5 residues within 4Å: Chain B: G.282, E.283, K.306, R.337, H.369 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.283, B:R.284 Water bridges: B:R.284 Salt bridges: B:K.306, B:R.337, B:H.369 SO4.15: 4 residues within 4Å: Chain B: R.135, S.136, A.137, R.284 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.136, B:A.137 Salt bridges: B:R.135, B:R.284, B:K.380 SO4.20: 5 residues within 4Å: Chain C: G.282, E.283, K.306, R.337, H.369 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.283 Water bridges: C:W.280 Salt bridges: C:K.306, C:R.337, C:H.369 SO4.21: 4 residues within 4Å: Chain C: R.135, S.136, A.137, R.284 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.136, C:A.137, C:A.137 Salt bridges: C:R.135, C:R.284 SO4.24: 2 residues within 4Å: Chain C: A.35, Q.36 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.36, C:Q.36 Water bridges: C:Q.37, C:Q.37 SO4.29: 5 residues within 4Å: Chain D: G.282, E.283, K.306, R.337, H.369 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.283, D:R.284 Water bridges: D:R.284 Salt bridges: D:K.306, D:R.337, D:H.369 SO4.32: 4 residues within 4Å: Chain D: R.135, S.136, A.137, R.284 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.136, D:A.137 Salt bridges: D:R.135, D:R.284, D:K.380

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: Q.70, P.120, V.121, V.122, E.242 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.242, A:E.242 Water bridges: A:K.123, A:K.123, A:E.242 GOL.8: 7 residues within 4Å: Chain A: E.63, M.180, T.187, E.242, I.243, Y.244, H.277 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.187, A:I.243, A:H.277 Water bridges: A:E.63, A:R.184 GOL.14: 6 residues within 4Å: Chain B: Q.70, P.120, V.121, V.122, Q.239, E.242 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.70, B:Q.239 Water bridges: B:K.123, B:K.123, B:E.242 GOL.16: 6 residues within 4Å: Chain B: E.63, R.66, T.187, A.241, E.242, I.243 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.66, B:T.187, B:T.187, B:T.187, B:I.243 GOL.22: 5 residues within 4Å: Chain C: Q.70, P.120, V.121, V.122, E.242 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.242 Water bridges: C:K.123, C:K.123, C:E.242 GOL.25: 7 residues within 4Å: Chain C: E.63, M.180, T.187, E.242, I.243, Y.244, H.277 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.187, C:T.187, C:I.243, C:H.277 Water bridges: C:E.63, C:E.63 GOL.31: 6 residues within 4Å: Chain D: Q.70, P.120, V.121, V.122, Q.239, E.242 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Q.70, D:Q.239, D:E.242 Water bridges: D:K.123, D:K.123, D:E.242 GOL.33: 6 residues within 4Å: Chain D: E.63, R.66, T.187, A.241, E.242, I.243 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.66, D:T.187, D:T.187, D:I.243

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

CL.6: 3 residues within 4Å: Chain A: V.60, P.61, S.62 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: P.17, L.18, R.23 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain B: V.60, P.61, S.62 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain C: V.60, P.61, S.62 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain D: P.17, L.18, R.23 Ligand excluded by PLIP CL.34: 3 residues within 4Å: Chain D: V.60, P.61, S.62 Ligand excluded by PLIP

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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