SMTL ID : 4zqr.1

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 8 residues within 4Å: Chain A: G.216, S.217, G.253, G.254, L.274, G.275, S.276, Y.299 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.217, A:G.254, A:G.275, A:S.276, A:Y.299 Water bridges: A:S.86, A:S.86, A:G.253, A:L.255, A:L.255, A:L.255, A:Q.256 PO4.12: 8 residues within 4Å: Chain B: G.216, S.217, G.253, G.254, L.274, G.275, S.276, Y.299 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.217, B:S.217, B:G.254, B:G.275, B:S.276, B:Y.299 Water bridges: B:S.86, B:S.86, B:G.253, B:L.255, B:S.276, B:S.276 PO4.22: 8 residues within 4Å: Chain C: G.216, S.217, G.253, G.254, L.274, G.275, S.276, Y.299 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.217, C:G.254, C:G.275, C:S.276 Water bridges: C:S.86, C:S.86, C:G.253, C:L.255, C:L.255, C:L.255, C:Q.256, C:L.277 PO4.30: 8 residues within 4Å: Chain D: G.216, S.217, G.253, G.254, L.274, G.275, S.276, Y.299 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:S.217, D:G.254, D:G.275, D:S.276, D:Y.299, D:Y.299 Water bridges: D:G.253, D:L.255, D:L.255, D:L.255, D:Q.256

15 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.2: 9 residues within 4Å: Chain A: P.64, A.361, G.364, Y.365 Chain D: A.163, H.164, K.332, E.336 Ligands: PGO.31 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:H.164 Hydrogen bonds: D:E.336, A:A.361 PGO.3: 6 residues within 4Å: Chain A: T.162, A.163, H.164, N.167, D.331 Ligands: PGO.23 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:H.164, A:N.167 Hydrogen bonds: A:T.162, A:A.163, A:H.164, A:D.331, A:D.331 PGO.4: 2 residues within 4Å: Chain A: R.360 Ligands: PGO.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.67, A:R.360 PGO.5: 5 residues within 4Å: Chain A: A.65, T.66, A.67, R.360 Ligands: PGO.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.66, A:A.67, A:R.360, A:R.360 PGO.13: 9 residues within 4Å: Chain B: P.64, A.361, G.364, Y.365 Chain C: A.163, H.164, K.332, E.336 Ligands: GOL.24 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:H.164 Hydrogen bonds: C:E.336, B:A.361, B:Y.365 PGO.14: 6 residues within 4Å: Chain B: T.162, A.163, H.164, N.167, D.331 Ligands: PGO.17 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:N.167 Hydrogen bonds: B:A.163, B:H.164, B:D.331 PGO.17: 9 residues within 4Å: Chain B: A.163, H.164, K.332, E.336 Chain D: P.64, A.361, G.364, Y.365 Ligands: PGO.14 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:H.164 Water bridges: B:K.332 Hydrogen bonds: D:A.361 PGO.18: 7 residues within 4Å: Chain B: D.52, T.383, P.384, L.387 Chain D: T.383, P.384, A.385 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:T.383, D:A.385 Hydrophobic interactions: B:P.384 PGO.21: 7 residues within 4Å: Chain B: T.383, P.384, A.385 Chain C: D.51, D.52, T.383, P.384 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.383, B:T.383, B:A.385 PGO.23: 9 residues within 4Å: Chain A: A.163, H.164, K.332, E.336 Chain C: P.64, A.361, G.364, Y.365 Ligands: PGO.3 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:H.164 Hydrogen bonds: C:A.361, C:Y.365 PGO.27: 5 residues within 4Å: Chain C: Q.256, Y.257, L.277, Y.404, Y.405 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.277 Hydrogen bonds: C:N.403, C:Y.405 PGO.28: 8 residues within 4Å: Chain A: T.383, P.384, A.385 Chain D: D.52, T.383, P.384, L.387 Ligands: GOL.10 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:P.384 Water bridges: D:D.51, D:D.51 Hydrogen bonds: A:T.383, A:A.385 PGO.31: 6 residues within 4Å: Chain D: T.162, A.163, H.164, N.167, D.331 Ligands: PGO.2 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:N.167 Hydrogen bonds: D:A.163, D:H.164, D:D.331 PGO.32: 2 residues within 4Å: Chain D: R.360 Ligands: PGO.33 No protein-ligand interaction detected (PLIP) PGO.33: 5 residues within 4Å: Chain D: A.65, T.66, A.67, R.360 Ligands: PGO.32 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.66, D:A.67, D:R.360, D:R.360

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: Q.256, Y.257, L.277, V.351, Q.354, L.355, P.402, Y.405 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.256 Water bridges: A:S.258, A:N.403 GOL.7: 9 residues within 4Å: Chain A: D.51, D.52, I.382, T.383, P.384, L.387 Chain C: T.383, P.384, A.385 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:I.382, C:T.383, C:A.385 GOL.8: 7 residues within 4Å: Chain A: D.51, Q.256, Y.257, D.260 Chain C: K.388, H.393, D.394 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:K.388, C:H.393, C:D.394, A:D.51, A:D.260 Water bridges: A:D.51 GOL.10: 5 residues within 4Å: Chain A: P.384 Chain B: P.384 Chain C: P.384 Chain D: P.384 Ligands: PGO.28 No protein-ligand interaction detected (PLIP) GOL.15: 7 residues within 4Å: Chain B: Q.256, Y.257, L.277, Q.354, L.355, P.402, Y.405 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.256, B:Y.405, B:Y.405 Water bridges: B:S.258, B:N.403 GOL.19: 7 residues within 4Å: Chain B: D.51, Q.256, Y.257, D.260 Chain D: K.388, H.393, D.394 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:D.260, D:K.388, D:K.388, D:D.394 GOL.24: 6 residues within 4Å: Chain B: V.63 Chain C: T.162, A.163, H.164, N.167 Ligands: PGO.13 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.163, C:H.164 Water bridges: C:N.167 GOL.25: 3 residues within 4Å: Chain C: D.68, S.70, R.78 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.68, C:S.70 Water bridges: C:R.78, C:R.78 GOL.26: 7 residues within 4Å: Chain B: K.388, H.393, D.394 Chain C: D.51, Q.256, Y.257, D.260 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:K.388, B:H.393, B:D.394, C:D.51, C:D.260 Water bridges: C:D.51 GOL.29: 7 residues within 4Å: Chain A: K.388, H.393, D.394 Chain D: D.51, Q.256, Y.257, D.260 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:K.388, A:D.394, D:D.51, D:D.260 Water bridges: D:D.51, D:D.51 GOL.34: 4 residues within 4Å: Chain D: Q.256, Y.257, L.277, Y.405 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.256, D:Y.405

4 x K: POTASSIUM ION(Non-covalent)

K.9: 7 residues within 4Å: Chain A: E.389, S.390, H.391 Chain D: G.214, P.215, G.216, C.219 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Metal complexes: D:G.214, D:G.216, D:C.219, A:E.389, A:S.390 K.11: 7 residues within 4Å: Chain A: G.214, P.215, G.216, C.219 Chain C: E.389, S.390, H.391 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Metal complexes: A:G.214, A:G.216, A:C.219, C:E.389, C:S.390 K.16: 7 residues within 4Å: Chain B: E.389, S.390, H.391 Chain C: G.214, P.215, G.216, C.219 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Metal complexes: C:G.214, C:G.216, C:C.219, B:E.389, B:S.390 K.20: 7 residues within 4Å: Chain B: G.214, P.215, G.216, C.219 Chain D: E.389, S.390, H.391 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Metal complexes: B:G.214, B:G.216, B:C.219, D:E.389, D:S.390

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Makowska-Grzyska, M. et al., Mycobacterium tuberculosis IMPDH in Complexes with Substrates, Products and Antitubercular Compounds. Plos One (2015)

Release Date

2015-06-17

Peptides

Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase

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