SMTL ID : 4fce.1

Crystal structure of Yersinia pestis GlmU in complex with alpha-D-glucosamine 1-phosphate (GP1)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-trimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.409 Chain B: D.409 Chain C: D.409 Ligands: MG.7, MG.13 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.409, C:D.409, B:D.409, H2O.3, H2O.16, H2O.29 MG.2: 8 residues within 4Å: Chain A: D.409, Q.411 Chain B: D.409, Q.411 Chain C: D.409, Q.411 Ligands: MG.8, MG.14 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.409, C:D.409, B:D.409, H2O.14, H2O.27, H2O.41 MG.7: 5 residues within 4Å: Chain A: D.409 Chain B: D.409 Chain C: D.409 Ligands: MG.1, MG.13 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.409, C:D.409, B:D.409, H2O.3, H2O.16, H2O.29 MG.8: 8 residues within 4Å: Chain A: D.409, Q.411 Chain B: D.409, Q.411 Chain C: D.409, Q.411 Ligands: MG.2, MG.14 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.409, C:D.409, B:D.409, H2O.14, H2O.27, H2O.41 MG.13: 5 residues within 4Å: Chain A: D.409 Chain B: D.409 Chain C: D.409 Ligands: MG.1, MG.7 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.409, C:D.409, B:D.409, H2O.3, H2O.16, H2O.29 MG.14: 8 residues within 4Å: Chain A: D.409, Q.411 Chain B: D.409, Q.411 Chain C: D.409, Q.411 Ligands: MG.2, MG.8 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.409, C:D.409, B:D.409, H2O.14, H2O.27, H2O.41

3 x GP1: 2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose(Non-covalent)

GP1.3: 9 residues within 4Å: Chain A: R.336, K.354, Y.369, N.389, Y.390, K.395 Chain C: K.363, H.366, N.380 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain C Hydrogen bonds: A:Y.369, A:Y.369, A:N.389, A:N.389, A:K.395, C:H.366, C:N.380, C:N.380 Water bridges: A:R.336, A:R.336, C:A.383 Salt bridges: A:R.336, A:K.354, A:K.395, A:K.395, C:H.366, C:H.366 GP1.9: 9 residues within 4Å: Chain A: K.363, H.366, N.380 Chain B: R.336, K.354, Y.369, N.389, Y.390, K.395 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:Y.369, B:Y.369, B:N.389, B:N.389, B:K.395, A:H.366, A:N.380, A:N.380 Water bridges: B:R.336, B:R.336, A:A.383 Salt bridges: B:R.336, B:K.354, B:K.395, B:K.395, A:H.366, A:H.366 GP1.15: 9 residues within 4Å: Chain B: K.363, H.366, N.380 Chain C: R.336, K.354, Y.369, N.389, Y.390, K.395 17 PLIP interactions: 6 interactions with chain B, 11 interactions with chain C Hydrogen bonds: B:H.366, B:N.380, B:N.380, C:Y.369, C:Y.369, C:N.389, C:N.389, C:K.395 Water bridges: B:A.383, C:R.336, C:R.336 Salt bridges: B:H.366, B:H.366, C:R.336, C:K.354, C:K.395, C:K.395

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

EDO.4: 5 residues within 4Å: Chain A: D.403, F.405, G.421, A.422, T.423 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.403, A:F.405 EDO.5: 7 residues within 4Å: Chain A: P.32, L.33, A.34, G.35, E.239, R.266 Chain C: L.258 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.34, A:G.35, A:E.239 Water bridges: A:R.266 EDO.6: 8 residues within 4Å: Chain A: D.278, R.294, G.296, T.297, P.314 Chain B: R.266, I.282, E.284 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.266, B:E.284, A:R.294, A:R.294, A:T.297 EDO.10: 5 residues within 4Å: Chain B: D.403, F.405, G.421, A.422, T.423 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.403, B:F.405 EDO.11: 7 residues within 4Å: Chain A: L.258 Chain B: P.32, L.33, A.34, G.35, E.239, R.266 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.34, B:G.35, B:E.239 Water bridges: B:R.266 EDO.12: 8 residues within 4Å: Chain B: D.278, R.294, G.296, T.297, P.314 Chain C: R.266, I.282, E.284 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.294, B:R.294, B:T.297, C:R.266, C:E.284 EDO.16: 5 residues within 4Å: Chain C: D.403, F.405, G.421, A.422, T.423 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.403, C:F.405 EDO.17: 7 residues within 4Å: Chain B: L.258 Chain C: P.32, L.33, A.34, G.35, E.239, R.266 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.34, C:G.35, C:E.239 Water bridges: C:R.266 EDO.18: 8 residues within 4Å: Chain A: R.266, I.282, E.284 Chain C: D.278, R.294, G.296, T.297, P.314 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:R.266, A:E.284, C:R.294, C:R.294, C:T.297

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nocek, B. et al., Crystal structure of Yersinia pestis GlmU in complex with alpha-D-glucosamine 1-phosphate (GP1). To be Published

Release Date

2012-07-11

Peptides

Bifunctional protein GlmU: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Bifunctional protein GlmU