- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.86 Å
- Oligo State
- homo-tetramer
- Ligands
- 10 x CA: CALCIUM ION(Non-covalent)
- 4 x XLS: D-xylose(Non-covalent)
XLS.3: 12 residues within 4Å:- Chain A: W.50, H.102, W.140, W.189, E.233, E.269, H.272, D.297, D.340
- Chain C: F.61
- Ligands: CA.1, CA.2
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:H.272, A:D.340
- Water bridges: A:T.142, A:T.142, A:E.269, A:D.340
XLS.13: 12 residues within 4Å:- Chain B: W.50, H.102, W.140, W.189, E.233, E.269, H.272, D.297, D.340
- Chain D: F.61
- Ligands: CA.11, CA.12
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:H.272, B:D.340, B:D.340
- Water bridges: B:T.142, B:A.143
XLS.18: 13 residues within 4Å:- Chain A: F.61
- Chain C: W.50, H.102, W.140, F.146, W.189, E.233, E.269, H.272, D.297, D.340
- Ligands: CA.16, CA.17
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:E.233, C:H.272
- Water bridges: C:T.142, C:A.143
XLS.25: 13 residues within 4Å:- Chain B: F.61
- Chain D: W.50, H.102, W.140, F.146, W.189, E.233, E.269, H.272, D.297, D.340
- Ligands: CA.23, CA.24
7 PLIP interactions:7 interactions with chain D- Hydrogen bonds: D:H.272, D:D.340, D:D.340
- Water bridges: D:T.142, D:A.143, D:E.269, D:D.340
- 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.5: 6 residues within 4Å:- Chain A: N.21, P.22, L.23, E.351
- Chain D: L.428
- Ligands: XYP.6
3 PLIP interactions:1 interactions with chain D, 2 interactions with chain A- Salt bridges: D:K.425
- Hydrogen bonds: A:E.351
- Water bridges: A:E.351
XYP.6: 5 residues within 4Å:- Chain A: Q.8, I.9, Q.10, L.23
- Ligands: XYP.5
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Q.8, A:Q.10, A:Q.10
XYP.10: 6 residues within 4Å:- Chain A: K.204, K.207, F.254, H.258
- Chain B: D.289, A.290
3 PLIP interactions:2 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:H.258
- Salt bridges: A:K.204
- Water bridges: B:D.289
XYP.14: 6 residues within 4Å:- Chain B: E.56, G.64, T.65, K.66, S.67
- Chain D: K.149
5 PLIP interactions:4 interactions with chain B, 1 interactions with chain D- Hydrogen bonds: B:E.56, B:E.56, B:K.66
- Water bridges: B:G.64
- Salt bridges: D:K.149
XYP.19: 5 residues within 4Å:- Chain A: K.149
- Chain C: E.56, G.64, K.66, S.67
2 PLIP interactions:1 interactions with chain C, 1 interactions with chain A- Hydrogen bonds: C:E.56
- Salt bridges: A:K.149
XYP.26: 5 residues within 4Å:- Chain B: K.149
- Chain D: E.56, G.64, K.66, S.67
4 PLIP interactions:3 interactions with chain D, 1 interactions with chain B- Hydrogen bonds: D:E.56, D:K.66
- Water bridges: D:G.64
- Salt bridges: B:K.149
XYP.27: 3 residues within 4Å:- Chain D: P.22, L.23, E.351
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:E.351
- 6 x SO4: SULFATE ION(Non-functional Binders)
SO4.7: 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
SO4.8: 5 residues within 4Å:- Chain A: S.112, I.113, E.114
- Chain B: G.417, E.418
5 PLIP interactions:3 interactions with chain B, 2 interactions with chain A- Water bridges: B:G.417, B:E.418, B:E.418, A:R.166
- Hydrogen bonds: A:I.113
SO4.15: 4 residues within 4Å:- Chain B: Q.8, D.349, L.350, E.351
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:L.350, B:E.351
- Water bridges: B:Q.8, B:Q.8
SO4.20: 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
SO4.21: 4 residues within 4Å:- Chain C: G.417, E.418
- Chain D: S.112, I.113
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
SO4.28: 3 residues within 4Å:- Chain D: D.349, L.350, E.351
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:L.350, D:E.351
- 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
- 10 x CA: CALCIUM ION(Non-covalent)
- 4 x XLS: D-xylose(Non-covalent)
- 8 x XYP: beta-D-xylopyranose(Non-covalent)
- 6 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