- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.11 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)
- 4 x ZN: ZINC ION(Non-covalent)
ZN.2: 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: 4 residues within 4Å:- Chain A: E.326, H.330
- Chain B: H.403, R.410
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:E.326, A:H.330
ZN.15: 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: 4 residues within 4Å:- Chain A: H.403, R.410
- 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.4
- 2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
PGE.3: 6 residues within 4Å:- Chain A: L.282, Y.317, E.343, R.344, E.347
- Ligands: EDO.6
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:Y.317, A:Y.317, A:E.343, A:R.344
- Water bridges: A:R.344
PGE.18: 5 residues within 4Å:- Chain B: F.255, N.256, K.258, V.259, H.260
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:N.256, B:V.259
- Water bridges: B:H.260
- 2 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)
NDG.4: 13 residues within 4Å:- Chain A: P.180, G.181, I.182, S.193, N.219, D.220, A.221, G.248, V.249, G.250, E.269, H.272, D.302
13 PLIP interactions:13 interactions with chain A- Hydrophobic interactions: A:I.182
- Hydrogen bonds: A:S.193, A:N.219, A:N.219, A:V.249, A:E.269, A:E.269, A:E.269
- Water bridges: A:S.193, A:G.248, A:G.248, A:G.251
- Salt bridges: A:H.272
NDG.21: 17 residues within 4Å:- Chain B: P.180, G.181, I.182, L.191, T.192, S.193, N.219, D.220, A.221, I.244, G.248, V.249, G.250, E.269, H.272, D.302
- Ligands: ANP.16
12 PLIP interactions:12 interactions with chain B- Hydrophobic interactions: B:I.182
- Hydrogen bonds: B:S.193, B:N.219, B:N.219, B:V.249, B:E.269, B:E.269
- Water bridges: B:N.194, B:N.194, B:G.251, B:H.272
- Salt bridges: B:H.272
- 15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.5: 5 residues within 4Å:- Chain A: R.235, G.236, E.237, N.256, G.257
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.256
- Water bridges: A:G.257
EDO.6: 6 residues within 4Å:- Chain A: L.283, N.287, H.316, Y.317
- Ligands: PGE.3, EDO.9
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:L.283, A:Y.317
EDO.7: 3 residues within 4Å:- Chain A: P.289, I.290, F.291
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:I.290
- Water bridges: A:H.316
EDO.8: 4 residues within 4Å:- Chain A: Y.331, E.343, E.380, R.384
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:E.380, A:R.384
EDO.9: 3 residues within 4Å:- Chain A: H.316, Y.317
- Ligands: EDO.6
No protein-ligand interaction detected (PLIP)EDO.10: 7 residues within 4Å:- Chain A: D.121, F.224, G.368, G.369, G.404, D.405, G.408
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:G.369, A:G.408
- Water bridges: A:D.121, A:A.406
EDO.11: 4 residues within 4Å:- Chain A: K.189, L.190, L.191, M.199
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:L.190
EDO.12: 3 residues within 4Å:- Chain A: F.318, R.336, R.337
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:F.318, A:R.336, A:R.336
EDO.22: 1 residues within 4Å:- Chain B: E.347
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:E.347
EDO.23: 3 residues within 4Å:- Chain B: E.237, H.363, K.397
No protein-ligand interaction detected (PLIP)EDO.24: 7 residues within 4Å:- Chain B: D.121, F.224, G.368, G.369, G.404, D.405, G.408
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:G.369, B:G.408
- Water bridges: B:D.121, B:S.372, B:S.372, B:A.406
EDO.25: 5 residues within 4Å:- Chain B: Y.331, E.343, L.376, E.380, R.384
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:Y.331, B:E.343
EDO.26: 2 residues within 4Å:- Chain B: K.296, N.297
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:K.296
EDO.27: 1 residues within 4Å:- Chain B: I.356
No protein-ligand interaction detected (PLIP)EDO.28: 4 residues within 4Å:- Chain B: L.282, L.283, Y.317, R.344
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:Y.317, B:Y.317, B:R.344
- 2 x K: POTASSIUM ION(Non-covalent)
K.13: 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.1, H2O.4
K.29: 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.6, H2O.9
- 3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.17: 4 residues within 4Å:- Chain B: P.386, A.387, L.389, H.391
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:A.387
PEG.19: 4 residues within 4Å:- Chain B: P.289, I.290, F.291, H.316
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:I.290, B:H.316
PEG.20: 3 residues within 4Å:- Chain B: F.318, R.336, R.337
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:R.336, B:R.336
- 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
BBBB
AAA
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.11 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)
- 4 x ZN: ZINC ION(Non-covalent)
- 2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- 2 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)
- 15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 2 x K: POTASSIUM ION(Non-covalent)
- 3 x PEG: DI(HYDROXYETHYL)ETHER(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
BBBB
AAA