SMTL ID : 2dft.1

Structure of shikimate kinase from Mycobacterium tuberculosis complexed with ADP and Mg at 2.8 angstrons of resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: S.16 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.16 MG.4: 3 residues within 4Å: Chain B: S.16, D.34 Ligands: ADP.6 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.16, H2O.3, H2O.4 MG.7: 3 residues within 4Å: Chain A: D.47 Chain C: S.16 Ligands: ADP.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.16 MG.9: 3 residues within 4Å: Chain D: S.16, D.32 Ligands: ADP.11 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.16

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

CL.2: 4 residues within 4Å: Chain A: P.11, K.15, G.80 Ligands: ADP.3 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain B: P.11, K.15, G.80 Ligands: ADP.6 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain D: P.11, K.15, G.80 Ligand excluded by PLIP

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 14 residues within 4Å: Chain A: L.10, P.11, G.12, S.13, G.14, K.15, S.16, T.17, R.110, R.153, P.155 Ligands: MG.1, CL.2, ADP.6 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.12, A:G.14, A:K.15, A:S.16, A:T.17, A:T.17, A:R.110, A:R.153 Water bridges: A:T.17, A:R.110, A:R.110 Salt bridges: A:K.15 pi-Cation interactions: A:R.110, A:R.110 ADP.6: 16 residues within 4Å: Chain A: P.155 Chain B: L.10, G.12, S.13, G.14, K.15, S.16, T.17, R.110, R.117, R.153, N.154, P.155 Ligands: ADP.3, MG.4, CL.5 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:G.12, B:S.13, B:G.14, B:G.14, B:K.15, B:S.16, B:T.17, B:T.17, B:T.17, B:R.110, B:R.153 Salt bridges: B:K.15, B:R.117, B:R.117 pi-Cation interactions: B:R.110, B:R.110 ADP.8: 17 residues within 4Å: Chain A: D.47 Chain C: L.10, P.11, G.12, S.13, G.14, K.15, S.16, T.17, R.110, T.150, R.153, N.154, P.155 Chain D: P.155 Ligands: MG.7, ADP.11 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:L.10, C:G.12, C:S.13, C:G.14, C:K.15, C:S.16, C:T.17, C:T.17, C:R.110, C:R.110, C:R.153 Salt bridges: C:K.15 pi-Cation interactions: C:R.110, C:R.110 ADP.11: 16 residues within 4Å: Chain C: P.155 Chain D: L.10, P.11, G.12, S.13, G.14, K.15, S.16, T.17, R.110, R.117, T.150, R.153, P.155 Ligands: ADP.8, MG.9 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:G.12, D:G.14, D:K.15, D:S.16, D:S.16, D:T.17, D:T.17, D:R.110, D:R.110, D:R.153 Water bridges: D:K.15, D:K.15 Salt bridges: D:K.15, D:R.117, D:R.117 pi-Cation interactions: D:R.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dias, M.V. et al., Effects of the magnesium and chloride ions and shikimate on the structure of shikimate kinase from Mycobacterium tuberculosis. ACTA CRYSTALLOGR.,SECT.F (2007)

Release Date

2007-01-16

Peptides

Shikimate kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Shikimate kinase

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