SMTL ID : 7p7w.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 18 residues within 4Å: Chain A: G.123, G.124, T.125, K.126, G.246, T.247, G.307, R.308, E.311, A.324, P.325, I.328, G.369, G.370, L.371, N.373 Ligands: IMD.3, IMD.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.124, A:T.125, A:K.126, A:T.247, A:T.247, A:G.307, A:A.324, A:G.370, A:N.373 Water bridges: A:G.248, A:N.373, A:N.373 ADP.24: 13 residues within 4Å: Chain B: G.246, T.247, G.307, R.308, E.311, A.324, P.325, I.328, G.369, G.370, L.371, N.373 Ligands: IMD.26 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.247, B:T.247, B:A.324, B:G.370 Water bridges: B:G.124, B:G.248, B:E.311, B:E.311, B:N.373

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: D.121, F.224, G.368, G.369, G.404, D.405, G.407, G.408 Ligands: IMD.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.121, A:G.369, A:G.404, A:G.407, A:G.408 Water bridges: A:D.121, A:S.372, A:S.372, A:A.406 GOL.5: 4 residues within 4Å: Chain A: Y.317, F.318, R.336, R.337 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.317, A:R.336, A:R.336, A:R.337 GOL.27: 10 residues within 4Å: Chain B: D.121, F.224, G.368, G.369, G.404, D.405, A.406, G.407, G.408 Ligands: IMD.26 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.121, B:G.369, B:D.405, B:G.407, B:G.408 Water bridges: B:S.372, B:G.404, B:V.409

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.3: 6 residues within 4Å: Chain A: D.121, D.220, I.244 Ligands: ADP.1, GOL.2, IMD.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.220, A:D.220 IMD.4: 5 residues within 4Å: Chain A: D.121, G.123, K.126 Ligands: ADP.1, IMD.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.121 Water bridges: A:E.128 IMD.25: 6 residues within 4Å: Chain A: H.391, V.392 Chain B: K.189, L.190, L.191, G.200 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.200 IMD.26: 6 residues within 4Å: Chain B: D.121, D.220, I.244, G.369 Ligands: ADP.24, GOL.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.220, B:D.220

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

NDG.6: 15 residues within 4Å: Chain A: P.180, G.181, I.182, L.191, T.192, S.193, N.219, D.220, A.221, G.248, V.249, G.250, E.269, H.272, D.302 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.182, A:L.191 Hydrogen bonds: A:S.193, A:S.193, A:N.219, A:N.219, A:E.269, A:E.269, A:E.269 Water bridges: A:N.194, A:I.195, A:G.248, A:H.272 Salt bridges: A:H.272 NDG.28: 11 residues within 4Å: Chain B: P.180, G.181, N.219, D.220, A.221, G.248, V.249, G.250, E.269, H.272, D.302 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.181, B:N.219, B:N.219, B:V.249, B:E.269, B:E.269, B:E.269 Water bridges: B:S.193, B:N.194, B:N.194, B:D.220, B:D.220, B:G.248 Salt bridges: B:H.272

4 x ZN: ZINC ION(Non-covalent)

ZN.7: 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.8: 2 residues within 4Å: Chain A: E.326, H.330 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.326, A:H.330 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 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.326, B:H.330

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

EDO.9: 4 residues within 4Å: Chain A: P.382, P.396, K.397, I.398 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: R.263 Chain B: L.395, K.397 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: V.137, V.139 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: P.289, I.290, F.291 Ligands: EDO.13 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: N.287, A.288, H.316 Ligands: EDO.12 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: E.375, Y.378, K.400 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: H.330, Q.333, E.335 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: Y.331, V.339 Ligands: PEG.21 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain A: K.281, L.282 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: D.315, H.316, S.319 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: G.114, T.115, M.116, V.171, K.172 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: K.296, N.297 Chain B: A.387 Ligand excluded by PLIP EDO.31: 2 residues within 4Å: Chain B: F.318, S.319 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain B: A.288, P.289, I.290, F.291 Ligands: EDO.35 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain B: E.208, Q.212, R.213, P.214 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain B: F.318, R.336, R.337 Ligand excluded by PLIP EDO.35: 2 residues within 4Å: Chain B: I.290 Ligands: EDO.32 Ligand excluded by PLIP

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

PEG.21: 7 residues within 4Å: Chain A: Y.331, E.343, L.376, Q.379, E.380, R.384 Ligands: EDO.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.379 Water bridges: A:Y.331, A:E.343

2 x K: POTASSIUM ION(Non-covalent)

K.22: 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.6, H2O.8 K.36: 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.19, H2O.20

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.23: 2 residues within 4Å: Chain A: N.355, C.359 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:T.273, B:T.273

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

2022-08-03

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

Related Entries With Identical Sequence