SMTL ID : 2oi7.2 (2 other biounits)

E. coli GlmU- Complex with UDP-GlcNAc, desulpho-CoA and GlcNAc-1-PO4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.54 Å

Oligo State

homo-trimer

Ligands

3 x GN1: 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose(Non-covalent)

GN1.1: 14 residues within 4Å: Chain A: K.360, H.363, N.377, G.379, A.380, S.405 Chain B: R.333, K.351, Y.366, T.384, N.386, Y.387, K.392 Ligands: DCA.6 17 PLIP interactions: 8 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:A.380, B:Y.366 Hydrogen bonds: A:H.363, A:N.377, A:N.377, A:A.380, B:Y.366, B:N.386, B:K.392 Water bridges: A:K.360 Salt bridges: A:H.363, A:H.363, B:R.333, B:K.351, B:K.351, B:K.392, B:K.392 GN1.8: 14 residues within 4Å: Chain B: K.360, H.363, N.377, G.379, A.380, S.405 Chain C: R.333, K.351, Y.366, T.384, N.386, Y.387, K.392 Ligands: DCA.13 17 PLIP interactions: 8 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:A.380, C:Y.366 Hydrogen bonds: B:H.363, B:N.377, B:N.377, B:A.380, C:Y.366, C:N.386, C:K.392 Water bridges: B:K.360 Salt bridges: B:H.363, B:H.363, C:R.333, C:K.351, C:K.351, C:K.392, C:K.392 GN1.15: 14 residues within 4Å: Chain A: R.333, K.351, Y.366, T.384, N.386, Y.387, K.392 Chain C: K.360, H.363, N.377, G.379, A.380, S.405 Ligands: DCA.20 17 PLIP interactions: 8 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: C:A.380, A:Y.366 Hydrogen bonds: C:H.363, C:N.377, C:N.377, C:A.380, A:Y.366, A:N.386, A:K.392 Water bridges: C:K.360 Salt bridges: C:H.363, C:H.363, A:R.333, A:K.351, A:K.351, A:K.392, A:K.392

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: K.25, D.105, N.227 Ligands: UD1.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.105, H2O.1, H2O.2 MG.9: 4 residues within 4Å: Chain B: K.25, D.105, N.227 Ligands: UD1.14 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.105, H2O.4, H2O.5 MG.16: 4 residues within 4Å: Chain C: K.25, D.105, N.227 Ligands: UD1.21 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.105, H2O.7, H2O.9

6 x CO: COBALT (II) ION(Non-covalent)

CO.3: 8 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: CO.4, CO.10, CO.11, CO.17, CO.18 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Metal complexes: C:D.406, A:D.406, B:D.406 CO.4: 8 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: CO.3, CO.10, CO.11, CO.17, CO.18 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A Metal complexes: B:D.406, B:D.406, C:D.406, C:D.406, A:D.406 CO.10: 8 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: CO.3, CO.4, CO.11, CO.17, CO.18 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Metal complexes: C:D.406, A:D.406, B:D.406 CO.11: 8 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: CO.3, CO.4, CO.10, CO.17, CO.18 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Metal complexes: B:D.406, C:D.406, C:D.406, A:D.406, A:D.406 CO.17: 8 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: CO.3, CO.4, CO.10, CO.11, CO.18 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Metal complexes: B:D.406, C:D.406, A:D.406 CO.18: 8 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: CO.3, CO.4, CO.10, CO.11, CO.17 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 interactions with chain C Metal complexes: B:D.406, B:D.406, A:D.406, C:D.406, C:D.406

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

SO4.5: 5 residues within 4Å: Chain A: K.15, G.16, T.17, R.18 Ligands: UD1.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.17, A:T.17, A:R.18 Water bridges: A:K.25, A:K.25 Salt bridges: A:R.18 SO4.12: 5 residues within 4Å: Chain B: K.15, G.16, T.17, R.18 Ligands: UD1.14 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.17, B:T.17, B:R.18 Water bridges: B:K.25, B:K.25 Salt bridges: B:R.18 SO4.19: 5 residues within 4Å: Chain C: K.15, G.16, T.17, R.18 Ligands: UD1.21 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.17, C:T.17, C:R.18 Water bridges: C:K.25, C:K.25 Salt bridges: C:R.18

3 x DCA: DESULFO-COENZYME A(Non-covalent)

DCA.6: 15 residues within 4Å: Chain A: F.402, G.404, S.405, A.422, A.423, I.438, R.440 Chain B: C.385, N.386, Y.387, V.410 Chain C: T.444, K.446, W.449 Ligands: GN1.1 14 PLIP interactions: 3 interactions with chain C, 8 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: C:W.449, A:A.422, A:A.423, B:Y.387, B:V.410 Hydrogen bonds: C:T.444, A:S.405, A:A.423, A:R.440, A:R.440, A:R.440, A:R.440, B:Y.387 Salt bridges: C:K.446 DCA.13: 15 residues within 4Å: Chain A: T.444, K.446, W.449 Chain B: F.402, G.404, S.405, A.422, A.423, I.438, R.440 Chain C: C.385, N.386, Y.387, V.410 Ligands: GN1.8 14 PLIP interactions: 8 interactions with chain B, 3 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: B:A.422, B:A.423, C:Y.387, C:V.410, A:W.449 Hydrogen bonds: B:S.405, B:A.423, B:R.440, B:R.440, B:R.440, B:R.440, C:Y.387, A:T.444 Salt bridges: A:K.446 DCA.20: 15 residues within 4Å: Chain A: C.385, N.386, Y.387, V.410 Chain B: T.444, K.446, W.449 Chain C: F.402, G.404, S.405, A.422, A.423, I.438, R.440 Ligands: GN1.15 14 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: A:Y.387, A:V.410, B:W.449, C:A.422, C:A.423 Hydrogen bonds: A:Y.387, B:T.444, C:S.405, C:A.423, C:R.440, C:R.440, C:R.440, C:R.440 Salt bridges: B:K.446

3 x UD1: URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE(Non-covalent)

UD1.7: 26 residues within 4Å: Chain A: L.11, A.12, A.13, G.14, R.18, K.25, Q.76, Q.79, L.80, G.81, T.82, A.85, Y.103, G.104, D.105, Y.139, G.140, E.154, N.169, T.170, Y.197, I.198, T.199, N.227 Ligands: MG.2, SO4.5 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:Y.197, A:T.199 Hydrogen bonds: A:A.13, A:G.14, A:G.14, A:R.18, A:Q.76, A:Q.76, A:G.81, A:T.82, A:G.104, A:D.105, A:G.140, A:E.154, A:E.154, A:N.169, A:N.169, A:T.170, A:N.227 Water bridges: A:K.25, A:K.25, A:Y.139 Salt bridges: A:K.25 UD1.14: 26 residues within 4Å: Chain B: L.11, A.12, A.13, G.14, R.18, K.25, Q.76, Q.79, L.80, G.81, T.82, A.85, Y.103, G.104, D.105, Y.139, G.140, E.154, N.169, T.170, Y.197, I.198, T.199, N.227 Ligands: MG.9, SO4.12 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Y.197, B:T.199 Hydrogen bonds: B:A.13, B:G.14, B:G.14, B:R.18, B:Q.76, B:Q.76, B:G.81, B:T.82, B:G.104, B:D.105, B:G.140, B:E.154, B:E.154, B:N.169, B:N.169, B:T.170, B:N.227 Water bridges: B:K.25, B:K.25, B:Y.139 Salt bridges: B:K.25 UD1.21: 26 residues within 4Å: Chain C: L.11, A.12, A.13, G.14, R.18, K.25, Q.76, Q.79, L.80, G.81, T.82, A.85, Y.103, G.104, D.105, Y.139, G.140, E.154, N.169, T.170, Y.197, I.198, T.199, N.227 Ligands: MG.16, SO4.19 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:Y.197, C:T.199 Hydrogen bonds: C:A.13, C:G.14, C:G.14, C:R.18, C:Q.76, C:Q.76, C:G.81, C:T.82, C:G.104, C:D.105, C:G.140, C:E.154, C:E.154, C:N.169, C:N.169, C:T.170, C:N.227 Water bridges: C:K.25, C:K.25, C:Y.139 Salt bridges: C:K.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Olsen, L.R. et al., Structure of the E. coli bifunctional GlmU acetyltransferase active site with substrates and products. Protein Sci. (2007)

Release Date

2007-06-19

Peptides

Bifunctional protein glmU: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

Bifunctional protein glmU

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