SMTL ID : 6ge9.1

Structure of Mycobacterium tuberculosis GlmU bound to Glc-1P and Ac-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-trimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 8 residues within 4Å: Chain A: S.392, D.417 Chain B: S.392, D.417 Chain C: S.392, D.417 Ligands: MG.9, MG.17 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 interactions with chain B Metal complexes: C:S.392, C:D.417, A:S.392, B:S.392, B:D.417 MG.9: 8 residues within 4Å: Chain A: S.392, D.417 Chain B: S.392, D.417 Chain C: S.392, D.417 Ligands: MG.1, MG.17 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 1 interactions with chain B Metal complexes: C:S.392, C:D.417, A:S.392, A:D.417, B:S.392 MG.17: 8 residues within 4Å: Chain A: S.392, D.417 Chain B: S.392, D.417 Chain C: S.392, D.417 Ligands: MG.1, MG.9 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 2 interactions with chain B Metal complexes: C:S.392, A:S.392, A:D.417, B:S.392, B:D.417

3 x G1P: 1-O-phosphono-alpha-D-glucopyranose(Non-covalent)

G1P.2: 9 residues within 4Å: Chain A: P.373, H.374, N.388 Chain B: R.344, K.362, Y.377, N.397, K.403 Ligands: ACO.3 13 PLIP interactions: 4 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:N.388, A:N.388, B:Y.377, B:Y.377, B:N.397, B:N.397 Water bridges: A:K.371 Salt bridges: A:H.374, B:R.344, B:K.362, B:K.362, B:K.403, B:K.403 G1P.10: 9 residues within 4Å: Chain B: P.373, H.374, N.388 Chain C: R.344, K.362, Y.377, N.397, K.403 Ligands: ACO.11 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain C Hydrogen bonds: B:N.388, B:N.388, C:Y.377, C:Y.377, C:N.397, C:N.397 Water bridges: B:K.371 Salt bridges: B:H.374, C:R.344, C:K.362, C:K.362, C:K.403, C:K.403 G1P.18: 9 residues within 4Å: Chain A: R.344, K.362, Y.377, N.397, K.403 Chain C: P.373, H.374, N.388 Ligands: ACO.19 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:Y.377, A:Y.377, A:N.397, A:N.397, C:N.388, C:N.388 Salt bridges: A:R.344, A:K.362, A:K.362, A:K.403, A:K.403, C:H.374 Water bridges: C:K.371

3 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.3: 26 residues within 4Å: Chain A: H.374, N.388, G.390, A.391, T.414, G.415, S.416, G.433, A.434, V.449, A.451 Chain B: Y.377, V.394, F.395, V.396, N.397, Y.398, V.421, V.437, R.439 Chain C: R.455, I.457, W.460, K.464, R.465 Ligands: G1P.2 15 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B, 4 interactions with chain C Hydrogen bonds: A:A.391, A:S.416, A:A.434, A:A.434, B:Y.398, B:R.439, C:R.455 Water bridges: A:A.451 Hydrophobic interactions: B:Y.377, B:V.394, B:V.396 pi-Cation interactions: B:R.439 Salt bridges: C:R.455, C:K.464, C:K.464 ACO.11: 26 residues within 4Å: Chain A: R.455, I.457, W.460, K.464, R.465 Chain B: H.374, N.388, G.390, A.391, T.414, G.415, S.416, G.433, A.434, V.449, A.451 Chain C: Y.377, V.394, F.395, V.396, N.397, Y.398, V.421, V.437, R.439 Ligands: G1P.10 15 PLIP interactions: 5 interactions with chain B, 6 interactions with chain C, 4 interactions with chain A Hydrogen bonds: B:A.391, B:S.416, B:A.434, B:A.434, C:Y.398, C:R.439, A:R.455 Water bridges: B:A.451 Hydrophobic interactions: C:Y.377, C:V.394, C:V.396 pi-Cation interactions: C:R.439 Salt bridges: A:R.455, A:K.464, A:K.464 ACO.19: 26 residues within 4Å: Chain A: Y.377, V.394, F.395, V.396, N.397, Y.398, V.421, V.437, R.439 Chain B: R.455, I.457, W.460, K.464, R.465 Chain C: H.374, N.388, G.390, A.391, T.414, G.415, S.416, G.433, A.434, V.449, A.451 Ligands: G1P.18 15 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: A:Y.377, A:V.394, A:V.396 Hydrogen bonds: A:Y.398, A:R.439, B:R.455, C:A.391, C:S.416, C:A.434, C:A.434 pi-Cation interactions: A:R.439 Salt bridges: B:R.455, B:K.464, B:K.464 Water bridges: C:A.451

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

PEG.4: 5 residues within 4Å: Chain A: F.148, G.149, Y.150, N.239, Q.243 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.239, A:Q.243 PEG.5: 4 residues within 4Å: Chain A: D.188, A.191, S.194, Q.222 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.194, A:S.194, A:Q.222 PEG.12: 5 residues within 4Å: Chain B: F.148, G.149, Y.150, N.239, Q.243 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.239, B:Q.243 PEG.13: 4 residues within 4Å: Chain B: D.188, A.191, S.194, Q.222 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.194, B:S.194, B:Q.222 PEG.20: 5 residues within 4Å: Chain C: F.148, G.149, Y.150, N.239, Q.243 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.239, C:Q.243 PEG.21: 4 residues within 4Å: Chain C: D.188, A.191, S.194, Q.222 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.194, C:S.194, C:Q.222

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 3 residues within 4Å: Chain A: H.29 Chain C: D.283, V.285 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.283, C:D.283 EDO.7: 1 residues within 4Å: Chain A: R.198 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.198 EDO.8: 4 residues within 4Å: Chain A: A.314, V.315, G.316, I.331 No protein-ligand interaction detected (PLIP) EDO.14: 3 residues within 4Å: Chain A: D.283, V.285 Chain B: H.29 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.283, A:D.283 EDO.15: 1 residues within 4Å: Chain B: R.198 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.198 EDO.16: 4 residues within 4Å: Chain B: A.314, V.315, G.316, I.331 No protein-ligand interaction detected (PLIP) EDO.22: 3 residues within 4Å: Chain B: D.283, V.285 Chain C: H.29 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.283, B:D.283 EDO.23: 1 residues within 4Å: Chain C: R.198 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.198 EDO.24: 4 residues within 4Å: Chain C: A.314, V.315, G.316, I.331 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Craggs, P.D. et al., The Mechanism of Acetyl Transfer Catalyzed by Mycobacterium tuberculosis GlmU. Biochemistry (2018)

Release Date

2018-05-02

Peptides

Bifunctional protein GlmU: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Bifunctional protein GlmU

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