SMTL ID : 2ypo.1

3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with phenylalanine bound in only one site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: C.87, H.369, 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.2 MN.8: 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.16: 4 residues within 4Å: Chain C: C.87, H.369, 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.17 MN.23: 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)

SO4.2: 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:K.306, A:R.337, A:H.369 Salt bridges: A:K.306, A:R.337, A:H.369 SO4.5: 4 residues within 4Å: Chain A: D.138, R.145, R.148, H.164 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.145, A:R.145 Salt bridges: A:R.145, A:R.148, A:H.164 SO4.9: 4 residues within 4Å: Chain B: R.23, L.26, E.53, R.256 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.53, B:E.53 Salt bridges: B:R.23, B:R.256 SO4.10: 6 residues within 4Å: Chain B: G.282, E.283, R.284, K.306, R.337, H.369 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.283, B:R.284 Water bridges: B:R.284, B:K.306, B:R.337 Salt bridges: B:K.306, B:R.337, B:H.369 SO4.14: 3 residues within 4Å: Chain B: R.135, S.136, A.137 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.136, B:S.136, B:A.137, B:R.284 Salt bridges: B:R.135 SO4.17: 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:K.306, C:R.337, C:H.369 Salt bridges: C:K.306, C:R.337, C:H.369 SO4.20: 4 residues within 4Å: Chain C: D.138, R.145, R.148, H.164 5 PLIP interactions: 5 interactions with chain C Water bridges: C:R.145, C:R.145 Salt bridges: C:R.145, C:R.148, C:H.164 SO4.24: 4 residues within 4Å: Chain D: R.23, L.26, E.53, R.256 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.53 Salt bridges: D:R.23, D:R.256 SO4.25: 6 residues within 4Å: Chain D: G.282, E.283, R.284, K.306, R.337, H.369 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:E.283, D:R.284 Water bridges: D:R.284, D:K.306, D:R.337 Salt bridges: D:K.306, D:R.337, D:H.369 SO4.29: 3 residues within 4Å: Chain D: R.135, S.136, A.137 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.136, D:S.136, D:A.137, D:R.284 Salt bridges: D:R.135

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: R.23, T.24, D.27 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.27 GOL.4: 4 residues within 4Å: Chain A: L.107, K.123, A.192, L.194 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.107, A:A.192 Water bridges: A:T.114, A:K.123, A:K.123, A:K.123 GOL.6: 7 residues within 4Å: Chain A: E.63, M.180, T.187, A.241, E.242, I.243, H.277 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.63, A:T.187, A:T.187, A:I.243, A:I.243 Water bridges: A:E.63, A:Y.244 GOL.11: 3 residues within 4Å: Chain B: R.25, Q.297, V.298 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.25, B:R.25, B:Q.297, B:Q.297 GOL.12: 9 residues within 4Å: Chain B: E.63, R.66, M.180, R.184, T.187, A.241, E.242, I.243, H.277 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.63, B:R.66, B:R.66, B:T.187, B:I.243 Water bridges: B:T.187 GOL.13: 6 residues within 4Å: Chain B: Q.70, P.120, V.121, V.122, Q.239, E.242 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.70, B:V.121, B:Q.239, B:Q.239, B:E.242, B:E.242 Water bridges: B:K.123, B:K.123 GOL.18: 3 residues within 4Å: Chain C: R.23, T.24, D.27 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.27, C:D.27 GOL.19: 4 residues within 4Å: Chain C: L.107, K.123, A.192, L.194 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:L.107, C:A.192 Water bridges: C:T.114, C:T.114, C:K.123, C:K.123 GOL.21: 7 residues within 4Å: Chain C: E.63, M.180, T.187, A.241, E.242, I.243, H.277 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.63, C:T.187, C:I.243, C:I.243 Water bridges: C:Y.244 GOL.26: 3 residues within 4Å: Chain D: R.25, Q.297, V.298 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.25, D:R.25, D:Q.297, D:Q.297 GOL.27: 9 residues within 4Å: Chain D: E.63, R.66, M.180, R.184, T.187, A.241, E.242, I.243, H.277 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.63, D:R.66, D:R.66, D:T.187, D:T.187, D:I.243 Water bridges: D:E.63 GOL.28: 6 residues within 4Å: Chain D: Q.70, P.120, V.121, V.122, Q.239, E.242 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Q.70, D:V.121, D:Q.239, D:Q.239, D:E.242 Water bridges: D:K.123, D:K.123

4 x PHE: PHENYLALANINE(Non-covalent)

PHE.7: 11 residues within 4Å: Chain A: F.91, M.92, R.171, A.174, N.175, A.178 Chain B: W.3, V.5, D.6, V.55, Y.173 11 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:A.174, A:A.178, B:W.3, B:V.55, B:Y.173 Hydrogen bonds: A:F.91, A:N.175, A:N.175, B:D.6, F.7 Salt bridges: A:R.171 PHE.15: 7 residues within 4Å: Chain A: V.55, Y.173 Chain B: F.91, R.171, A.174, N.175, A.178 11 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: B:A.174, B:A.178, A:V.55 Hydrogen bonds: B:F.91, B:N.175, B:N.175, F.15 Water bridges: B:R.171, F.15 Salt bridges: B:R.171 pi-Stacking: A:Y.173 PHE.22: 11 residues within 4Å: Chain C: F.91, M.92, R.171, A.174, N.175, A.178 Chain D: W.3, V.5, D.6, V.55, Y.173 11 PLIP interactions: 6 interactions with chain C, 4 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: C:A.174, C:A.178, D:W.3, D:V.55, D:Y.173 Hydrogen bonds: C:F.91, C:N.175, C:N.175, D:D.6, F.22 Salt bridges: C:R.171 PHE.30: 7 residues within 4Å: Chain C: V.55, Y.173 Chain D: F.91, R.171, A.174, N.175, A.178 11 PLIP interactions: 7 interactions with chain D, 2 interactions with chain C, 2 Ligand-Ligand interactions Hydrophobic interactions: D:A.174, D:A.178, C:V.55 Hydrogen bonds: D:F.91, D:N.175, D:N.175, F.30 Water bridges: D:R.171, F.30 Salt bridges: D:R.171 pi-Stacking: C:Y.173

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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