- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.75 Å
- Oligo State
- homo-dimer
- Ligands
- 22 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.3: 3 residues within 4Å:- Chain A: Y.331, E.332, V.339
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:E.332
PEG.22: 4 residues within 4Å:- Chain A: N.297
- Chain B: A.387, H.388
- Ligands: TRS.28
2 PLIP interactions:2 interactions with chain B- Water bridges: B:E.347, B:H.388
PEG.23: 4 residues within 4Å:- Chain B: P.386, L.389, L.390, A.393
1 PLIP interactions:1 interactions with chain B- Water bridges: B:L.395
PEG.26: 6 residues within 4Å:- Chain B: D.233, L.234, E.237, V.364, K.397, R.402
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:E.237, B:K.397
PEG.30: 4 residues within 4Å:- Chain B: L.282, E.343, E.347, R.384
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:E.343, B:E.343
- Water bridges: B:E.347, B:E.347, B:E.347
PEG.35: 3 residues within 4Å:- Chain B: Y.331, E.332, G.334
No protein-ligand interaction detected (PLIP)PEG.36: 5 residues within 4Å:- Chain B: N.194, P.292, C.293, G.294, R.308
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:G.294
- Water bridges: B:R.308
- 2 x 4QY: 2-acetamido-2-deoxy-6-O-phosphono-beta-D-glucopyranose(Non-covalent)
4QY.4: 22 residues within 4Å:- Chain A: G.124, P.180, G.181, I.182, L.191, T.192, S.193, N.194, N.219, D.220, A.221, I.244, G.246, T.247, G.248, V.249, G.250, E.269, H.272, D.302
- Ligands: EDO.6, CL.21
15 PLIP interactions:15 interactions with chain A- Hydrophobic interactions: A:I.182
- Hydrogen bonds: A:G.124, A:S.193, A:S.193, A:N.194, A:N.219, A:D.220, A:G.246, A:T.247, A:G.248, A:E.269, A:E.269
- Water bridges: A:I.195, A:G.251
- Salt bridges: A:H.272
4QY.27: 20 residues within 4Å:- Chain B: P.180, G.181, I.182, L.191, T.192, S.193, N.194, N.219, D.220, A.221, I.244, G.246, T.247, G.248, V.249, G.250, E.269, H.272, D.302
- Ligands: PO4.41
16 PLIP interactions:16 interactions with chain B- Hydrophobic interactions: B:I.182
- Hydrogen bonds: B:S.193, B:S.193, B:N.194, B:N.219, B:D.220, B:G.246, B:T.247, B:G.248, B:E.269, B:E.269
- Water bridges: B:I.195, B:D.220, B:D.220, B:G.251
- Salt bridges: B:H.272
- 4 x ZN: ZINC ION(Non-covalent)
ZN.15: 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.16: 2 residues within 4Å:- Chain A: E.326, H.330
1 PLIP interactions:1 interactions with chain A- Metal complexes: A:H.330
ZN.38: 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.39: 2 residues within 4Å:- Chain B: E.326, H.330
1 PLIP interactions:1 interactions with chain B- Metal complexes: B:H.330
- 2 x K: POTASSIUM ION(Non-covalent)
K.18: 4 residues within 4Å:- Chain A: N.219, N.222, G.251, A.267
4 PLIP interactions:2 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:G.251, A:A.267, H2O.3, H2O.5
K.40: 4 residues within 4Å:- Chain B: N.219, N.222, G.251, A.267
4 PLIP interactions:2 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:G.251, B:A.267, H2O.11, H2O.12
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.20: 7 residues within 4Å:- Chain A: T.273, N.355, C.359
- Chain B: T.273, N.355, I.356, C.359
3 PLIP interactions:3 interactions with chain A- Water bridges: A:T.273, A:T.273, A:R.274
PO4.41: 6 residues within 4Å:- Chain B: G.123, G.124, G.246, T.247
- Ligands: 4QY.27, EDO.32
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:G.124, B:T.247, B:T.247, B:T.247
- Water bridges: B:T.125
- 1 x CL: CHLORIDE ION(Non-functional Binders)
- 1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- 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
AAAB
BBB
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.75 Å
- Oligo State
- homo-dimer
- Ligands
- 22 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 2 x 4QY: 2-acetamido-2-deoxy-6-O-phosphono-beta-D-glucopyranose(Non-covalent)
- 4 x ZN: ZINC ION(Non-covalent)
- 2 x K: POTASSIUM ION(Non-covalent)
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
- 1 x CL: CHLORIDE ION(Non-functional Binders)
- 1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- 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
AAAB
BBB