SMTL ID : 7p7i.1

Native structure of N-acetylglucosamine kinase from Plesiomonas shigelloides

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

PEG.1: 4 residues within 4Å: Chain A: A.134, W.230, R.235, L.417 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.135 PEG.2: 4 residues within 4Å: Chain A: P.292, C.293, G.294, R.308 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.294 Water bridges: A:R.308 PEG.11: 2 residues within 4Å: Chain B: A.134, W.230 No protein-ligand interaction detected (PLIP)

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 8 residues within 4Å: Chain A: T.273, N.355, I.356, C.359 Chain B: T.273, N.355, I.356, C.359 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Water bridges: B:T.273, B:R.274, B:C.352, A:R.274 Hydrogen bonds: A:T.273, A:T.273, A:N.355

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 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.12: 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

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

PGE.5: 6 residues within 4Å: Chain A: L.191, E.269, H.272, G.294, C.295 Chain B: V.392 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.191, A:G.294 PGE.13: 4 residues within 4Å: Chain A: L.390 Chain B: G.181, L.191, H.272 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.191

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

EDO.6: 3 residues within 4Å: Chain A: D.121, E.128, D.405 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.405 Water bridges: A:D.121, A:D.121, A:D.121, A:D.405 EDO.7: 8 residues within 4Å: Chain A: E.128, F.129, R.141, E.142, R.143, D.405, A.406, V.409 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.129, A:R.141, A:E.142, A:D.405 Water bridges: A:V.409 EDO.8: 6 residues within 4Å: Chain A: A.324, I.328, G.370, L.371, N.373, F.374 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.373, A:N.373 EDO.9: 2 residues within 4Å: Chain A: S.193, N.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.194 EDO.14: 3 residues within 4Å: Chain B: P.180, D.220, D.405 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.220, B:D.405 EDO.15: 3 residues within 4Å: Chain B: Y.151, L.155, D.206 No protein-ligand interaction detected (PLIP) EDO.16: 5 residues within 4Å: Chain B: F.224, G.368, G.369, G.404, D.405 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.369 Water bridges: B:S.372, B:D.405, B:D.405 EDO.17: 4 residues within 4Å: Chain B: D.233, R.235, G.236, E.237 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.236 Water bridges: B:D.233, B:D.233

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

CL.10: 3 residues within 4Å: Chain A: F.132, R.138, R.410 Ligand excluded by PLIP

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

2022-07-27

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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