- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.86 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x CD: CADMIUM ION(Non-covalent)
- 2 x XLS: D-xylose(Non-covalent)
XLS.3: 13 residues within 4Å:- Chain A: W.50, H.102, W.140, F.146, W.189, E.233, E.269, H.272, D.297, D.340
- Chain C: F.61
- Ligands: CD.1, CD.2
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:H.102
- Water bridges: A:H.51, A:W.189, A:E.269
XLS.12: 14 residues within 4Å:- Chain B: W.50, H.102, W.140, F.146, W.189, E.233, E.269, H.272, D.297, D.308, D.340
- Chain D: F.61
- Ligands: CD.10, CD.11
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:H.102
- Water bridges: B:H.51, B: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 C: K.149
4 PLIP interactions:3 interactions with chain A, 1 interactions with chain C- Hydrogen bonds: A:E.56, A:K.66
- Water bridges: A:G.64
- Salt bridges: C:K.149
XYP.6: 4 residues within 4Å:- Chain A: P.22, E.351
- Chain D: L.428
- Ligands: XYP.7
4 PLIP interactions:3 interactions with chain A, 1 interactions with chain D- Hydrogen bonds: A:E.351, A:E.351
- Water bridges: A:E.351
- Salt bridges: D:K.425
XYP.7: 5 residues within 4Å:- Chain A: Q.8, I.9, Q.10, L.23
- Ligands: XYP.6
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:Q.10, A:Q.10
- Water bridges: A:N.21, A:N.21, A:N.21
XYP.13: 6 residues within 4Å:- Chain B: E.56, G.64, T.65, K.66, S.67
- Chain D: K.149
7 PLIP interactions:6 interactions with chain B, 1 interactions with chain D- Hydrogen bonds: B:E.56, B:E.56, B:K.66, D:K.149
- Water bridges: B:G.64, B:G.64, B:G.64
XYP.15: 3 residues within 4Å:- Chain B: P.22, E.351
- Chain C: L.428
4 PLIP interactions:3 interactions with chain B, 1 interactions with chain C- Hydrogen bonds: B:E.351, B:E.351
- Water bridges: B:N.21
- Salt bridges: C:K.425
XYP.21: 6 residues within 4Å:- Chain A: K.149
- Chain C: E.56, G.64, T.65, K.66, S.67
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain A- Hydrogen bonds: C:E.56
- Water bridges: C:G.64, C:G.64
- Salt bridges: A:K.149
XYP.23: 6 residues within 4Å:- Chain C: K.40, D.41, R.44, P.97, Y.98, K.137
10 PLIP interactions:10 interactions with chain C- Hydrogen bonds: C:D.41, C:Y.98, C:K.137
- Water bridges: C:K.40, C:R.44, C:R.44, C:F.45, C:K.137
- Salt bridges: C:R.44, C:K.137
XYP.29: 3 residues within 4Å:- Chain D: P.22, L.23, E.351
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:E.351, D:E.351
- Water bridges: D:N.21, D:N.21
- 6 x XYS: alpha-D-xylopyranose(Non-covalent)
XYS.5: 6 residues within 4Å:- Chain A: K.204, K.207, F.254, H.258
- Chain B: D.289, A.290
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:H.258
- Water bridges: B:D.289
XYS.14: 6 residues within 4Å:- Chain A: D.289, A.290
- Chain B: K.204, K.207, F.254, H.258
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:H.258
XYS.20: 12 residues within 4Å:- Chain C: W.50, H.102, W.140, F.146, W.189, E.233, E.269, H.272, D.297, D.340
- Ligands: CD.18, CD.19
1 PLIP interactions:1 interactions with chain C- Salt bridges: C:H.102
XYS.22: 6 residues within 4Å:- Chain C: K.204, K.207, F.254, H.258
- Chain D: D.289, A.290
2 PLIP interactions:1 interactions with chain C, 1 interactions with chain D- Hydrogen bonds: C:H.258
- Water bridges: D:D.289
XYS.27: 12 residues within 4Å:- Chain D: W.50, H.102, W.140, F.146, W.189, E.233, E.269, H.272, D.297, D.340
- Ligands: CD.25, CD.26
1 PLIP interactions:1 interactions with chain D- Salt bridges: D:H.102
XYS.28: 6 residues within 4Å:- Chain C: D.289, A.290
- Chain D: K.204, K.207, F.254, H.258
2 PLIP interactions:1 interactions with chain D, 1 interactions with chain C- Hydrogen bonds: D:H.258
- Water bridges: C:A.290
- 8 x SO4: SULFATE ION(Non-functional Binders)
SO4.8: 4 residues within 4Å:- Chain A: S.112, I.113
- Chain B: G.417, E.418
6 PLIP interactions:3 interactions with chain A, 3 interactions with chain B- Hydrogen bonds: A:I.113
- Water bridges: A:E.114, A:R.166, B:K.414, B:E.418, B:E.418
SO4.9: 3 residues within 4Å:- Chain A: D.349, L.350, E.351
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:L.350, A:E.351
- Water bridges: A:Q.8, A:Q.8, A:E.351, A:E.351
SO4.16: 4 residues within 4Å:- Chain B: Q.8, D.349, L.350, E.351
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:Q.8, B:L.350, B:E.351
SO4.17: 4 residues within 4Å:- Chain A: G.417, E.418
- Chain B: S.112, I.113
4 PLIP interactions:2 interactions with chain B, 2 interactions with chain A- Hydrogen bonds: B:I.113
- Water bridges: B:R.166, A:G.417, A:E.418
SO4.24: 3 residues within 4Å:- Chain C: D.349, L.350, E.351
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:L.350, C:E.351
- Water bridges: C:Q.8, C:E.351, C:E.351
SO4.30: 5 residues within 4Å:- Chain C: S.112, I.113, E.114
- Chain D: G.417, E.418
3 PLIP interactions:2 interactions with chain C, 1 interactions with chain D- Hydrogen bonds: C:I.113
- Water bridges: C:R.166, D:E.418
SO4.31: 3 residues within 4Å:- Chain D: D.349, L.350, E.351
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:L.350, D:E.351
- Water bridges: D:Q.8
SO4.32: 5 residues within 4Å:- Chain C: G.417, E.418
- Chain D: S.112, I.113, E.114
3 PLIP interactions:2 interactions with chain D, 1 interactions with chain C- Hydrogen bonds: D:I.113
- Water bridges: D:R.166, C:E.418
- 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 1.86 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x CD: CADMIUM ION(Non-covalent)
- 2 x XLS: D-xylose(Non-covalent)
- 8 x XYP: beta-D-xylopyranose(Non-covalent)
- 6 x XYS: alpha-D-xylopyranose(Non-covalent)
- 8 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