- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.08 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x MN: MANGANESE (II) ION(Non-covalent)
- 4 x XLS: D-xylose(Non-covalent)
XLS.3: 14 residues within 4Å:- Chain A: W.50, H.102, W.140, W.189, E.233, K.235, E.269, H.272, D.297, D.308, D.340
- Chain D: F.61
- Ligands: MN.1, MN.2
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:H.102
- Water bridges: A:T.142, A:E.269, A:D.340
XLS.10: 14 residues within 4Å:- Chain B: W.50, H.102, W.140, W.189, E.233, K.235, E.269, H.272, D.297, D.308, D.340
- Chain C: F.61
- Ligands: MN.8, MN.9
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:H.102
- Water bridges: B:H.51, B:E.269
XLS.17: 14 residues within 4Å:- Chain B: F.61
- Chain C: W.50, H.102, W.140, W.189, E.233, K.235, E.269, H.272, D.297, D.308, D.340
- Ligands: MN.15, MN.16
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:H.102, C:E.233, C:D.340
- Water bridges: C:H.51, C:E.269
XLS.22: 15 residues within 4Å:- Chain A: F.61
- Chain D: W.50, H.102, W.140, F.146, W.189, E.233, K.235, E.269, H.272, D.297, D.308, D.340
- Ligands: MN.20, MN.21
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:H.102
- Water bridges: D:H.51, D:E.269
- 8 x XYP: beta-D-xylopyranose(Non-covalent)
XYP.4: 6 residues within 4Å:- Chain A: E.56, G.64, T.65, K.66, S.67
- Chain D: K.149
3 PLIP interactions:1 interactions with chain D, 2 interactions with chain A- Salt bridges: D:K.149
- Hydrogen bonds: A:E.56, A:K.66
XYP.5: 5 residues within 4Å:- Chain A: K.204, K.207, H.258
- Chain C: D.289, A.290
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain C- Hydrogen bonds: A:H.258
- Water bridges: C:E.249
XYP.6: 6 residues within 4Å:- Chain A: D.289, A.290
- Chain C: K.204, K.207, F.254, H.258
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:K.204, C:H.258
- Salt bridges: C:H.258
XYP.11: 6 residues within 4Å:- Chain B: K.40, D.41, R.44, P.97, Y.98, K.137
8 PLIP interactions:8 interactions with chain B- Hydrogen bonds: B:K.40, B:R.44, B:Y.98
- Water bridges: B:K.40, B:D.41, B:D.41, B:Y.98
- Salt bridges: B:K.40
XYP.12: 5 residues within 4Å:- Chain B: D.289, A.290
- Chain D: K.204, K.207, H.258
4 PLIP interactions:2 interactions with chain D, 2 interactions with chain B- Hydrogen bonds: D:H.258
- Salt bridges: D:H.258
- Water bridges: B:D.289, B:D.289
XYP.14: 5 residues within 4Å:- Chain C: K.40, D.41, R.44, Y.98, K.137
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:K.40, C:D.41, C:R.44, C:Y.98
- Water bridges: C:Y.98, C:Y.98
- Salt bridges: C:K.137
XYP.19: 6 residues within 4Å:- Chain B: K.204, K.207, F.254, H.258
- Chain D: D.289, A.290
5 PLIP interactions:4 interactions with chain B, 1 interactions with chain D- Hydrogen bonds: B:H.258
- Water bridges: B:K.204, B:K.204, D:K.256
- Salt bridges: B:H.258
XYP.23: 5 residues within 4Å:- Chain D: K.40, D.41, R.44, Y.98, K.137
8 PLIP interactions:8 interactions with chain D- Hydrogen bonds: D:K.40, D:D.41, D:D.41, D:R.44, D:Y.98
- Water bridges: D:R.44, D:G.135
- Salt bridges: D:K.137
- 3 x SO4: SULFATE ION(Non-functional Binders)
SO4.7: 4 residues within 4Å:- Chain A: S.112, I.113
- Chain C: G.417, E.418
5 PLIP interactions:2 interactions with chain C, 3 interactions with chain A- Water bridges: C:K.414, C:G.417, A:E.114, A:R.166
- Hydrogen bonds: A:I.113
SO4.13: 4 residues within 4Å:- Chain B: S.112, I.113
- Chain D: G.417, E.418
4 PLIP interactions:3 interactions with chain B, 1 interactions with chain D- Hydrogen bonds: B:I.113
- Water bridges: B:E.114, B:R.166, D:E.418
SO4.18: 5 residues within 4Å:- Chain A: G.417, E.418
- Chain C: S.112, I.113, E.114
3 PLIP interactions:1 interactions with chain A, 2 interactions with chain C- Hydrogen bonds: A:E.418, C:I.113
- Water bridges: C:R.166
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Lee, M. et al., Metal Dependence of the Xylose Isomerase from Piromyces sp. E2 Explored by Activity Profiling and Protein Crystallography. Biochemistry (2017)
- Release Date
- 2017-11-01
- Peptides
- Xylose isomerase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.08 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x MN: MANGANESE (II) ION(Non-covalent)
- 4 x XLS: D-xylose(Non-covalent)
- 8 x XYP: beta-D-xylopyranose(Non-covalent)
- 3 x SO4: SULFATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Lee, M. et al., Metal Dependence of the Xylose Isomerase from Piromyces sp. E2 Explored by Activity Profiling and Protein Crystallography. Biochemistry (2017)
- Release Date
- 2017-11-01
- Peptides
- Xylose isomerase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D