SMTL ID : 6pbj.1

The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase with Gly190Pro mutation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 6 residues within 4Å: Chain A: G.284, E.285, R.286, K.308, R.339, H.371 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.285, A:R.286 Water bridges: A:E.250, A:W.282, A:R.286, A:K.308 Salt bridges: A:K.308, A:R.339, A:H.371 PO4.11: 5 residues within 4Å: Chain B: G.284, E.285, K.308, R.339, H.371 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.285 Water bridges: B:R.286, B:R.286, B:K.308 Salt bridges: B:K.308, B:R.339, B:H.371 PO4.22: 6 residues within 4Å: Chain C: G.284, E.285, R.286, K.308, R.339, H.371 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:E.285, C:R.286 Water bridges: C:E.250, C:W.282, C:R.286, C:K.308 Salt bridges: C:K.308, C:R.339, C:H.371 PO4.32: 5 residues within 4Å: Chain D: G.284, E.285, K.308, R.339, H.371 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.285 Water bridges: D:R.286, D:R.286, D:K.308 Salt bridges: D:K.308, D:R.339, D:H.371

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

SO4.2: 5 residues within 4Å: Chain A: V.62, P.63, S.64 Chain B: R.102, P.192 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Water bridges: B:R.102, B:S.191 Salt bridges: B:R.102 Hydrogen bonds: A:S.64, A:S.64, A:S.64 SO4.3: 2 residues within 4Å: Chain A: A.37, Q.38 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.38 Water bridges: A:A.36, A:Q.38, A:Q.39 SO4.4: 4 residues within 4Å: Chain A: T.41, R.147, R.150, H.166 8 PLIP interactions: 8 interactions with chain A Water bridges: A:R.147, A:R.147, A:S.148, A:R.150, A:R.150 Salt bridges: A:R.147, A:R.150, A:H.166 SO4.12: 3 residues within 4Å: Chain B: R.25, L.28, R.258 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.258 Salt bridges: B:R.25, B:R.258 SO4.13: 5 residues within 4Å: Chain A: R.102, P.192 Chain B: V.62, P.63, S.64 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Water bridges: A:R.102, A:R.102, A:S.191 Salt bridges: A:R.102 Hydrogen bonds: B:S.64, B:S.64 SO4.14: 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 SO4.23: 5 residues within 4Å: Chain C: V.62, P.63, S.64 Chain D: R.102, P.192 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:S.64, C:S.64, C:S.64 Water bridges: D:R.102, D:S.191 Salt bridges: D:R.102 SO4.24: 2 residues within 4Å: Chain C: A.37, Q.38 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.38 Water bridges: C:A.36, C:Q.38, C:Q.39 SO4.25: 4 residues within 4Å: Chain C: T.41, R.147, R.150, H.166 8 PLIP interactions: 8 interactions with chain C Water bridges: C:R.147, C:R.147, C:S.148, C:R.150, C:R.150 Salt bridges: C:R.147, C:R.150, C:H.166 SO4.33: 3 residues within 4Å: Chain D: R.25, L.28, R.258 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.258 Salt bridges: D:R.25, D:R.258 SO4.34: 5 residues within 4Å: Chain C: R.102, P.192 Chain D: V.62, P.63, S.64 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Water bridges: C:R.102, C:R.102, C:S.191 Salt bridges: C:R.102 Hydrogen bonds: D:S.64, D:S.64 SO4.35: 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

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

MN.5: 5 residues within 4Å: Chain A: C.89, H.371, R.384, E.413, D.443 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.89, A:H.371, A:E.413, A:E.413, A:D.443 MN.15: 3 residues within 4Å: Chain B: C.89, H.371, E.413 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.89, B:H.371, B:E.413, B:E.413 MN.26: 5 residues within 4Å: Chain C: C.89, H.371, R.384, E.413, D.443 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:C.89, C:H.371, C:E.413, C:E.413, C:D.443 MN.36: 3 residues within 4Å: Chain D: C.89, H.371, E.413 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.89, D:H.371, D:E.413, D:E.413

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

CL.6: 5 residues within 4Å: Chain A: G.341, N.342, H.343, K.344, R.388 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: R.27, H.328 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: R.170, R.173 Chain B: P.10 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: R.51, R.258 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain B: R.27, H.328 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain B: G.341, N.342, H.343, R.388 Ligand excluded by PLIP CL.27: 5 residues within 4Å: Chain C: G.341, N.342, H.343, K.344, R.388 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain C: R.27, H.328 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain C: R.170, R.173 Chain D: P.10 Ligand excluded by PLIP CL.37: 2 residues within 4Å: Chain D: R.51, R.258 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain D: R.27, H.328 Ligand excluded by PLIP CL.39: 4 residues within 4Å: Chain D: G.341, N.342, H.343, R.388 Ligand excluded by PLIP

8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 7 residues within 4Å: Chain A: E.65, R.186, T.189, A.243, E.244, I.245, H.279 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.65, A:R.186, A:A.243, A:I.245 Water bridges: A:T.189 PEG.19: 3 residues within 4Å: Chain B: A.36, A.37, Q.38 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.38 Water bridges: B:A.37, B:Q.39 PEG.20: 6 residues within 4Å: Chain A: P.63, R.262, L.263, L.276 Chain B: E.98, R.102 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.98, B:R.102 Water bridges: A:L.263 PEG.21: 8 residues within 4Å: Chain B: E.65, M.182, R.186, T.189, A.243, E.244, I.245, H.279 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.65, B:T.189, B:A.243, B:I.245 Water bridges: B:E.244 PEG.30: 7 residues within 4Å: Chain C: E.65, R.186, T.189, A.243, E.244, I.245, H.279 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.65, C:R.186, C:T.189, C:A.243, C:I.245 Water bridges: C:E.65 PEG.40: 3 residues within 4Å: Chain D: A.36, A.37, Q.38 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.38 Water bridges: D:A.37, D:Q.39 PEG.41: 6 residues within 4Å: Chain C: P.63, R.262, L.263, L.276 Chain D: E.98, R.102 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:E.98, D:R.102 Water bridges: C:L.263 PEG.42: 8 residues within 4Å: Chain D: E.65, M.182, R.186, T.189, A.243, E.244, I.245, H.279 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.65, D:A.243, D:I.245 Water bridges: D:T.189

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.10: 9 residues within 4Å: Chain A: I.9, F.93, V.172, R.173, A.176, N.177 Chain B: I.9, V.53, V.57 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.173, A:R.173, A:N.177 PG4.31: 9 residues within 4Å: Chain C: I.9, F.93, V.172, R.173, A.176, N.177 Chain D: I.9, V.53, V.57 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.173, C:R.173, C:N.177

Links

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Citation

Jiao, W. et al., A single amino acid substitution uncouples catalysis and allostery in an essential biosynthetic enzyme in Mycobacterium tuberculosis . J.Biol.Chem. (2020)

Release Date

2020-04-08

Peptides

Phospho-2-dehydro-3-deoxyheptonate aldolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Phospho-2-dehydro-3-deoxyheptonate aldolase