- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x MG: MAGNESIUM 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 B: F.61
- Ligands: MG.1, MG.2
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:H.102, A:E.233, A:H.272
- Water bridges: A:H.51, A:T.142, A:D.340
XLS.11: 14 residues within 4Å:- Chain A: F.61
- Chain B: W.50, H.102, W.140, W.189, E.233, K.235, E.269, H.272, D.297, D.308, D.340
- Ligands: MG.9, MG.10
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:H.102, B:E.233, B:H.272
- Water bridges: B:H.51, B:D.340
XLS.19: 14 residues within 4Å:- Chain C: 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: MG.17, MG.18
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:H.102, C:E.233, C:D.340
- Water bridges: C:W.50, C:H.51, C:H.102, C:D.340
XLS.27: 14 residues within 4Å:- Chain C: F.61
- Chain D: W.50, H.102, W.140, W.189, E.233, K.235, E.269, H.272, D.297, D.308, D.340
- Ligands: MG.25, MG.26
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:H.102, D:E.233, D:D.340
- Water bridges: D:H.51, D:D.340
- 6 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 B: K.149
5 PLIP interactions:4 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:E.56, A:K.66
- Water bridges: A:G.64, A:G.64
- Salt bridges: B:K.149
XYP.12: 6 residues within 4Å:- Chain A: K.149
- Chain B: E.56, G.64, T.65, K.66, S.67
4 PLIP interactions:3 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:E.56, B:K.66
- Water bridges: B:G.64
- Salt bridges: A:K.149
XYP.20: 6 residues within 4Å:- Chain C: E.56, G.64, T.65, K.66, S.67
- Chain D: K.149
5 PLIP interactions:1 interactions with chain D, 4 interactions with chain C- Salt bridges: D:K.149
- Hydrogen bonds: C:E.56, C:E.56, C:K.66
- Water bridges: C:G.64
XYP.22: 3 residues within 4Å:- Chain A: L.428
- Chain C: P.22, E.351
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:E.351
XYP.28: 6 residues within 4Å:- Chain C: K.149
- Chain D: E.56, G.64, T.65, K.66, S.67
6 PLIP interactions:5 interactions with chain D, 1 interactions with chain C- Hydrogen bonds: D:E.56, D:K.66, C:K.149
- Water bridges: D:E.56, D:G.64, D:G.64
XYP.31: 5 residues within 4Å:- Chain B: L.428
- Chain D: N.21, P.22, L.23, E.351
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:E.351
- 8 x XYS: alpha-D-xylopyranose(Non-covalent)
XYS.5: 6 residues within 4Å:- Chain A: K.40, D.41, R.44, P.97, Y.98, K.137
8 PLIP interactions:8 interactions with chain A- Hydrogen bonds: A:Y.98
- Water bridges: A:K.40, A:K.40, A:R.44, A:K.137, A:K.137
- Salt bridges: A:R.44, A:K.137
XYS.6: 4 residues within 4Å:- Chain A: P.22, L.23, E.351
- Chain C: L.428
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:E.351
- Water bridges: A:E.351
XYS.13: 6 residues within 4Å:- Chain B: K.204, K.207, F.254, H.258
- Chain C: D.289, A.290
2 PLIP interactions:1 interactions with chain C, 1 interactions with chain B- Water bridges: C:D.289
- Hydrogen bonds: B:H.258
XYS.14: 6 residues within 4Å:- Chain B: K.40, D.41, R.44, P.97, Y.98, K.137
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:Y.98
- Water bridges: B:R.44
- Salt bridges: B:R.44, B:K.137
XYS.15: 4 residues within 4Å:- Chain B: P.22, L.23, E.351
- Chain D: L.428
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:E.351
- Water bridges: B:E.351
XYS.21: 6 residues within 4Å:- Chain B: D.289, A.290
- Chain C: K.204, K.207, F.254, H.258
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:H.258
XYS.29: 6 residues within 4Å:- Chain A: D.289, A.290
- Chain D: K.204, K.207, F.254, H.258
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:H.258
XYS.30: 5 residues within 4Å:- Chain D: K.40, D.41, R.44, Y.98, K.137
9 PLIP interactions:9 interactions with chain D- Water bridges: D:K.40, D:K.40, D:R.44, D:Y.98, D:Y.98, D:K.137, D:K.137
- Salt bridges: D:R.44, D:K.137
- 7 x SO4: SULFATE ION(Non-functional Binders)
SO4.7: 4 residues within 4Å:- Chain A: Q.8, D.349, L.350, E.351
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:Q.8, A:L.350, A:E.351
- Water bridges: A:E.351, A:E.351
SO4.8: 4 residues within 4Å:- Chain A: S.112, I.113
- Chain D: G.417, E.418
5 PLIP interactions:3 interactions with chain A, 2 interactions with chain D- Hydrogen bonds: A:I.113
- Water bridges: A:E.114, A:R.166, D:E.418, D:E.418
SO4.16: 5 residues within 4Å:- Chain B: S.112, I.113, E.114
- Chain C: G.417, E.418
5 PLIP interactions:2 interactions with chain B, 3 interactions with chain C- Hydrogen bonds: B:I.113
- Water bridges: B:R.166, C:G.417, C:G.417, C:E.418
SO4.23: 4 residues within 4Å:- Chain B: G.417, E.418
- Chain C: S.112, I.113
6 PLIP interactions:4 interactions with chain C, 2 interactions with chain B- Hydrogen bonds: C:I.113
- Water bridges: C:E.114, C:E.114, C:R.166, B:G.417, B:E.418
SO4.24: 4 residues within 4Å:- Chain C: Q.8, D.349, L.350, E.351
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:Q.8, C:L.350, C:E.351
SO4.32: 5 residues within 4Å:- Chain A: G.417, E.418
- Chain D: S.112, I.113, E.114
5 PLIP interactions:3 interactions with chain A, 2 interactions with chain D- Hydrogen bonds: A:G.417, D:I.113
- Water bridges: A:G.417, A:E.418, D:R.166
SO4.33: 4 residues within 4Å:- Chain D: Q.8, D.349, L.350, E.351
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:Q.8, D:E.351
- Water bridges: D:L.350, D:L.350
- 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 1.90 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x MG: MAGNESIUM ION(Non-covalent)
- 4 x XLS: D-xylose(Non-covalent)
- 6 x XYP: beta-D-xylopyranose(Non-covalent)
- 8 x XYS: alpha-D-xylopyranose(Non-covalent)
- 7 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