SMTL ID : 7kr9.1

Bifunctional enzyme GlmU bound to Zn(II)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

6 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.2: 5 residues within 4Å: Chain A: N.405 Chain B: N.405 Chain C: N.405 Ligands: CA.7, CA.12 No protein-ligand interaction detected (PLIP) CA.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.7: 5 residues within 4Å: Chain A: N.405 Chain B: N.405 Chain C: N.405 Ligands: CA.2, CA.12 No protein-ligand interaction detected (PLIP) CA.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.12: 5 residues within 4Å: Chain A: N.405 Chain B: N.405 Chain C: N.405 Ligands: CA.2, CA.7 No protein-ligand interaction detected (PLIP)

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

ACO.3: 20 residues within 4Å: Chain A: Y.365, I.382, T.383, V.384, N.385, Y.386, I.409 Chain B: K.445, Y.448 Chain C: H.362, G.378, A.379, F.401, G.403, S.404, G.421, A.422, I.437, R.439, R.441 19 PLIP interactions: 13 interactions with chain C, 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: C:A.379, C:F.401, C:I.437, A:Y.365, A:I.382, A:V.384 Hydrogen bonds: C:A.379, C:S.404, C:A.422, C:R.439, C:R.439, C:R.439, C:R.441, A:Y.386 Water bridges: C:N.376, C:R.439, A:N.385 pi-Cation interactions: C:R.441 Salt bridges: B:K.445 ACO.8: 20 residues within 4Å: Chain A: H.362, G.378, A.379, F.401, G.403, S.404, G.421, A.422, I.437, R.439, R.441 Chain B: Y.365, I.382, T.383, V.384, N.385, Y.386, I.409 Chain C: K.445, Y.448 19 PLIP interactions: 13 interactions with chain A, 5 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: A:A.379, A:F.401, A:I.437, B:Y.365, B:I.382, B:V.384 Hydrogen bonds: A:A.379, A:S.404, A:A.422, A:R.439, A:R.439, A:R.439, A:R.441, B:Y.386 Water bridges: A:N.376, A:R.439, B:N.385 pi-Cation interactions: A:R.441 Salt bridges: C:K.445 ACO.13: 20 residues within 4Å: Chain A: K.445, Y.448 Chain B: H.362, G.378, A.379, F.401, G.403, S.404, G.421, A.422, I.437, R.439, R.441 Chain C: Y.365, I.382, T.383, V.384, N.385, Y.386, I.409 19 PLIP interactions: 5 interactions with chain C, 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: C:Y.365, C:I.382, C:V.384, B:A.379, B:F.401, B:I.437 Hydrogen bonds: C:Y.386, B:A.379, B:S.404, B:A.422, B:R.439, B:R.439, B:R.439, B:R.441 Water bridges: C:N.385, B:N.376, B:R.439 pi-Cation interactions: B:R.441 Salt bridges: A:K.445

3 x ZN: ZINC ION(Non-covalent)

ZN.4: 2 residues within 4Å: Chain A: E.315, H.330 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.315, A:E.315, A:H.330, H2O.10, H2O.10 ZN.9: 2 residues within 4Å: Chain B: E.315, H.330 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.315, B:E.315, B:H.330, H2O.20, H2O.21 ZN.14: 2 residues within 4Å: Chain C: E.315, H.330 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.315, C:E.315, C:H.330, H2O.31, H2O.32

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: D.300, T.302, E.316, S.317 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.300, A:T.302, A:T.302, A:T.302 GOL.10: 4 residues within 4Å: Chain B: D.300, T.302, E.316, S.317 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.300, B:T.302, B:T.302, B:T.302 GOL.15: 4 residues within 4Å: Chain C: D.300, T.302, E.316, S.317 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.300, C:T.302, C:T.302, C:T.302

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brazel, E.B. et al., Dysregulation of Streptococcus pneumoniae zinc homeostasis breaks ampicillin resistance in a pneumonia infection model. Cell Rep (2022)

Release Date

2021-12-01

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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