SMTL ID : 7p9y.1

N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 8 residues within 4Å: Chain A: G.246, T.247, G.307, E.311, A.324, G.370, L.371 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.324 MPD.11: 3 residues within 4Å: Chain A: D.233, G.236, E.237 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.233 MPD.21: 8 residues within 4Å: Chain B: L.245, G.246, T.247, G.307, A.324, P.325, G.370, L.371 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.325 Hydrogen bonds: B:G.307, B:G.370, B:L.371

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

EDO.2: 7 residues within 4Å: Chain A: G.181, I.182, A.183, I.217, E.218, N.219, N.265 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: R.263 Chain B: E.237, P.238, H.363 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: I.244, G.246, T.247, G.369, G.370 Ligands: MPD.1 Ligand excluded by PLIP EDO.6: 1 residues within 4Å: Chain A: N.256 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: K.281, M.285 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: D.315, H.316, S.319 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: E.320, L.322, E.326 Ligands: ZN.14 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain A: H.330, E.335 Ligand excluded by PLIP EDO.16: 2 residues within 4Å: Chain A: G.334, V.339 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain B: G.181, I.182, A.183, I.217, E.218, N.219, N.265 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain A: L.191, C.295, K.296 Chain B: L.390, H.391, V.392 Ligand excluded by PLIP EDO.23: 2 residues within 4Å: Chain B: K.394, L.395 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain B: P.292, C.293, G.294 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain B: H.330, E.335 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain B: E.375, K.400 Ligands: EDO.27 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: I.399, K.400 Ligands: EDO.26 Ligand excluded by PLIP

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 5 residues within 4Å: Chain A: I.328, E.332, N.373, F.374, E.375 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.375

2 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG.12: 11 residues within 4Å: Chain A: G.181, L.191, N.219, D.220, A.221, G.248, V.249, G.250, E.269, H.272, D.302 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.191 Hydrogen bonds: A:G.181, A:N.219, A:N.219, A:V.249, A:E.269, A:E.269, A:H.272 NDG.28: 12 residues within 4Å: Chain B: G.181, I.182, L.191, N.219, D.220, A.221, G.248, V.249, G.250, E.269, H.272, D.302 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.182, B:L.191 Hydrogen bonds: B:G.181, B:N.219, B:N.219, B:A.221, B:V.249, B:E.269, B:E.269, B:E.269 Salt bridges: B:H.272

4 x ZN: ZINC ION(Non-covalent)

ZN.13: 4 residues within 4Å: Chain A: H.272, C.293, C.295, C.300 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.272, A:C.293, A:C.295, A:C.300 ZN.14: 3 residues within 4Å: Chain A: E.326, H.330 Ligands: EDO.9 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.326, A:H.330, H2O.5 ZN.29: 4 residues within 4Å: Chain B: H.272, C.293, C.295, C.300 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.272, B:C.293, B:C.295, B:C.300 ZN.30: 2 residues within 4Å: Chain B: E.326, H.330 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.326, B:H.330, H2O.9

2 x K: POTASSIUM ION(Non-covalent)

K.15: 5 residues within 4Å: Chain A: N.219, N.222, G.251, A.267, G.268 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.251, A:A.267, H2O.2, H2O.4 K.31: 5 residues within 4Å: Chain B: N.219, N.222, G.251, A.267, G.268 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.251, B:A.267, H2O.8, H2O.8

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.17: 1 residues within 4Å: Chain A: R.336 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain A: E.343, E.380, R.384 Ligand excluded by PLIP

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

PEG.19: 8 residues within 4Å: Chain A: F.255, N.256, K.258 Chain B: F.255, N.256, K.258, V.259, H.260 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:K.258, A:V.259 Hydrogen bonds: B:N.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cross, A.R. et al., Spinning sugars in antigen biosynthesis: characterization of the Coxiella burnetii and Streptomyces griseus TDP-sugar epimerases. J.Biol.Chem. (2022)

Release Date

2022-08-10

Peptides

Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase

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