- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x NI: NICKEL (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 C: F.61
- Ligands: NI.1, NI.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.11: 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 D: F.61
- Ligands: NI.9, NI.10
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:H.102
- Water bridges: B:E.269, B:D.340
XLS.21: 14 residues within 4Å:- Chain A: 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: NI.19, NI.20
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:H.102
- Water bridges: C:T.142, C:E.269, C:D.340
XLS.29: 14 residues within 4Å:- Chain B: 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: NI.27, NI.28
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:H.102
- Water bridges: D:E.269, D:D.340
- 10 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:1 interactions with chain C, 3 interactions with chain A- Salt bridges: C:K.149
- Hydrogen bonds: A:E.56, A:K.66
- Water bridges: A:G.64
XYP.6: 3 residues within 4Å:- Chain A: P.22, E.351
- Chain D: L.428
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:E.351
- Water bridges: A:E.351
XYP.7: 6 residues within 4Å:- Chain A: D.289, A.290
- Chain B: K.204, K.207, F.254, H.258
4 PLIP interactions:3 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:K.204, B:H.258
- Salt bridges: B:H.258
- Water bridges: A:E.249
XYP.12: 6 residues within 4Å:- Chain B: E.56, G.64, T.65, K.66, S.67
- Chain D: K.149
7 PLIP interactions:5 interactions with chain B, 2 interactions with chain D- Hydrogen bonds: B:E.56, B:K.66, B:K.66, D:K.149, D:K.149
- Water bridges: B:G.64, B:G.64
XYP.13: 5 residues within 4Å:- Chain B: K.40, D.41, R.44, Y.98, K.137
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:K.40, B:D.41, B:R.44, B:Y.98
- Water bridges: B:Y.98, B:Y.98
- Salt bridges: B:K.137
XYP.14: 4 residues within 4Å:- Chain B: P.22, L.23, E.351
- Chain C: L.428
4 PLIP interactions:1 interactions with chain C, 3 interactions with chain B- Salt bridges: C:K.425
- Hydrogen bonds: B:E.351, B:E.351
- Water bridges: B:N.21
XYP.16: 6 residues within 4Å:- Chain B: K.149
- Chain D: E.56, G.64, T.65, K.66, S.67
6 PLIP interactions:3 interactions with chain D, 3 interactions with chain B- Hydrogen bonds: D:K.66, D:K.66, B:K.149, B:K.149
- Water bridges: D:G.64
- Salt bridges: B:K.149
XYP.23: 6 residues within 4Å:- Chain C: K.40, D.41, R.44, P.97, Y.98, K.137
9 PLIP interactions:9 interactions with chain C- Hydrogen bonds: C:R.44, C:Y.98, C:K.137
- Water bridges: C:K.40, C:R.44, C:G.135, C:K.137
- Salt bridges: C:K.40, C:K.137
XYP.24: 3 residues within 4Å:- Chain B: L.428
- Chain C: P.22, E.351
5 PLIP interactions:4 interactions with chain C, 1 interactions with chain B- Hydrogen bonds: C:E.351, C:E.351
- Water bridges: C:N.21, C:E.351
- Salt bridges: B:K.425
XYP.32: 4 residues within 4Å:- Chain A: L.428
- Chain D: P.22, L.23, E.351
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:E.351
- Water bridges: D:N.21, D:E.351
- 5 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.15: 4 residues within 4Å:- Chain A: K.204
- Chain B: V.288, D.289, R.328
8 PLIP interactions:1 interactions with chain A, 7 interactions with chain B- Water bridges: A:K.204, B:G.291, B:R.328, B:R.328, B:R.328, B:R.328
- Hydrogen bonds: B:D.289
- Salt bridges: B:R.328
XYS.22: 6 residues within 4Å:- Chain C: K.204, K.207, F.254, H.258
- Chain D: D.289, A.290
6 PLIP interactions:4 interactions with chain C, 2 interactions with chain D- Hydrogen bonds: C:K.204, C:K.204, C:H.258
- Salt bridges: C:K.204
- Water bridges: D:K.256, D:D.289
XYS.30: 6 residues within 4Å:- Chain C: D.289, A.290
- Chain D: K.204, K.207, F.254, H.258
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:K.204, D:K.204, D:H.258
- Salt bridges: D:K.204
XYS.31: 6 residues within 4Å:- Chain D: K.40, D.41, R.44, P.97, Y.98, K.137
5 PLIP interactions:5 interactions with chain D- Water bridges: D:R.44, D:Y.98, D:K.137
- Salt bridges: D:R.44, D:K.137
- 5 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
8 PLIP interactions:4 interactions with chain B, 4 interactions with chain A- Water bridges: B:K.414, B:E.418, B:E.418, B:E.418, A:E.114, A:E.114, A:R.166
- Hydrogen bonds: A:I.113
SO4.17: 4 residues within 4Å:- Chain A: G.417, E.418
- Chain B: S.112, I.113
7 PLIP interactions:4 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:I.113
- Water bridges: B:N.111, B:E.114, B:R.166, A:G.417, A:E.418, A:E.418
SO4.18: 3 residues within 4Å:- Chain B: D.349, L.350, E.351
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:L.350, B:E.351
SO4.25: 5 residues within 4Å:- Chain C: S.112, I.113, E.114
- Chain D: G.417, E.418
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:I.113
- Water bridges: C:R.166
SO4.26: 4 residues within 4Å:- Chain C: G.417, E.418
- Chain D: S.112, I.113
6 PLIP interactions:3 interactions with chain D, 3 interactions with chain C- Hydrogen bonds: D:I.113
- Water bridges: D:E.114, D:R.166, C:G.417, C:E.418, 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 1.80 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x NI: NICKEL (II) ION(Non-covalent)
- 4 x XLS: D-xylose(Non-covalent)
- 10 x XYP: beta-D-xylopyranose(Non-covalent)
- 5 x XYS: alpha-D-xylopyranose(Non-covalent)
- 5 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