SMTL ID : 7pa1.1

Structure of N-acetylglucosamine kinase from Plesiomonas shigelloides in complex with AMP-PNP in the absence of N-acetylglucoseamine substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

PEG.1: 3 residues within 4Å: Chain A: E.208, Q.212, R.213 No protein-ligand interaction detected (PLIP) PEG.9: 7 residues within 4Å: Chain B: D.184, T.187, K.189, L.190, L.191, M.199, G.200 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.187, B:T.187, B:L.190

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 13 residues within 4Å: Chain A: I.244, G.246, T.247, G.307, R.308, E.311, A.324, P.325, I.328, G.369, G.370, L.371, N.373 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.247, A:T.247, A:T.247, A:E.311, A:A.324, A:G.370, A:N.373 ANP.10: 13 residues within 4Å: Chain B: I.244, G.246, T.247, G.307, R.308, E.311, A.324, P.325, I.328, G.369, G.370, L.371, N.373 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.247, B:T.247, B:E.311, B:A.324, B:G.370, B:N.373

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 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.11: 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

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

PGE.4: 12 residues within 4Å: Chain A: F.255, K.258, V.259, H.260, S.261, G.262 Chain B: P.238, S.239, F.255, N.256, H.363 Ligands: EDO.17 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.260, A:S.261, A:G.262, B:N.256 Water bridges: B:N.256 PGE.5: 3 residues within 4Å: Chain A: A.134, L.136, W.230 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.235 PGE.12: 7 residues within 4Å: Chain A: L.390, V.392 Chain B: L.191, E.269, H.272, G.294, C.295 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.191 PGE.13: 5 residues within 4Å: Chain B: A.134, W.230, N.256, L.417 Ligands: EDO.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.134, B:L.417

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

EDO.6: 4 residues within 4Å: Chain A: D.233, R.235, G.236, E.237 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.233 Water bridges: A:E.237, A:E.237 EDO.7: 4 residues within 4Å: Chain A: E.375, Y.378, I.399, K.400 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.375, A:K.400 Water bridges: A:E.375, A:K.400 EDO.8: 2 residues within 4Å: Chain A: H.272 Chain B: L.390 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.272 EDO.14: 4 residues within 4Å: Chain B: R.235, G.236, E.237 Ligands: EDO.18 No protein-ligand interaction detected (PLIP) EDO.15: 7 residues within 4Å: Chain A: P.238, N.256, H.363 Chain B: V.259, H.260, S.261, G.262 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.261, B:S.261, B:G.262, A:N.256 Water bridges: B:K.258, B:V.259 EDO.16: 8 residues within 4Å: Chain B: A.229, L.234, R.235, G.236, E.237, N.256, G.257 Ligands: PGE.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.236, B:E.237 Water bridges: B:G.257 EDO.17: 4 residues within 4Å: Chain A: N.256 Chain B: F.255, K.258 Ligands: PGE.4 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:F.255, A:N.256 Water bridges: B:F.255 EDO.18: 5 residues within 4Å: Chain A: R.263 Chain B: E.237, P.238, H.363 Ligands: EDO.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.237 EDO.19: 4 residues within 4Å: Chain B: T.174, V.175, R.213, P.214 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.175, B:P.214

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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