- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.10 Å
- Oligo State
- homo-tetramer
- Ligands
- 48 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 4 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)
IPA.13: 4 residues within 4Å:- Chain A: F.360, D.361, A.365
- Chain D: D.110
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.361
- Water bridges: A:D.361
IPA.32: 4 residues within 4Å:- Chain B: F.360, D.361, A.365
- Chain C: D.110
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:D.361
- Water bridges: B:D.361
IPA.51: 4 residues within 4Å:- Chain B: D.110
- Chain C: F.360, D.361, A.365
3 PLIP interactions:1 interactions with chain B, 2 interactions with chain C- Water bridges: B:D.110, C:D.361
- Hydrogen bonds: C:D.361
IPA.70: 4 residues within 4Å:- Chain A: D.110
- Chain D: F.360, D.361, A.365
3 PLIP interactions:2 interactions with chain D, 1 interactions with chain A- Hydrogen bonds: D:D.361
- Water bridges: D:D.361, A:D.110
- 8 x MN: MANGANESE (II) ION(Non-covalent)
MN.14: 5 residues within 4Å:- Chain A: E.217, H.220, N.247, D.255, D.257
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.255, A:D.255, A:D.257, A:D.257, H2O.4
MN.15: 6 residues within 4Å:- Chain A: E.181, E.217, D.245, D.287
- Ligands: EDO.1, MG.16
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287, H2O.6
MN.33: 5 residues within 4Å:- Chain B: E.217, H.220, N.247, D.255, D.257
5 PLIP interactions:4 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.255, B:D.255, B:D.257, B:D.257, H2O.24
MN.34: 6 residues within 4Å:- Chain B: E.181, E.217, D.245, D.287
- Ligands: EDO.20, MG.35
5 PLIP interactions:4 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287, H2O.26
MN.52: 5 residues within 4Å:- Chain C: E.217, H.220, N.247, D.255, D.257
5 PLIP interactions:4 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.255, C:D.255, C:D.257, C:D.257, H2O.44
MN.53: 6 residues within 4Å:- Chain C: E.181, E.217, D.245, D.287
- Ligands: EDO.39, MG.54
5 PLIP interactions:4 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287, H2O.46
MN.71: 5 residues within 4Å:- Chain D: E.217, H.220, N.247, D.255, D.257
5 PLIP interactions:4 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:D.255, D:D.255, D:D.257, D:D.257, H2O.64
MN.72: 6 residues within 4Å:- Chain D: E.181, E.217, D.245, D.287
- Ligands: EDO.58, MG.73
5 PLIP interactions:4 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:E.181, D:E.217, D:D.245, D:D.287, H2O.66
- 8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
MG.16: 6 residues within 4Å:- Chain A: E.181, E.217, D.245, D.287
- Ligands: EDO.1, MN.15
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287, H2O.6
MG.17: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.35: 6 residues within 4Å:- Chain B: E.181, E.217, D.245, D.287
- Ligands: EDO.20, MN.34
5 PLIP interactions:4 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287, H2O.26
MG.36: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.54: 6 residues within 4Å:- Chain C: E.181, E.217, D.245, D.287
- Ligands: EDO.39, MN.53
5 PLIP interactions:4 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287, H2O.46
MG.55: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.73: 6 residues within 4Å:- Chain D: E.181, E.217, D.245, D.287
- Ligands: EDO.58, MN.72
5 PLIP interactions:4 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:E.181, D:E.217, D:D.245, D:D.287, H2O.66
MG.74: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)- 8 x NA: SODIUM ION(Non-functional Binders)
NA.18: 4 residues within 4Å:- Chain A: L.236, G.239, K.240, L.241
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:G.239, A:L.241
- Water bridges: A:G.239
NA.19: 5 residues within 4Å:- Chain A: D.153, D.156, R.157
- Chain D: A.339
- Ligands: EDO.6
4 PLIP interactions:3 interactions with chain A, 1 interactions with chain D- Hydrogen bonds: A:D.156, A:R.157, A:R.157, D:A.339
NA.37: 4 residues within 4Å:- Chain B: L.236, G.239, K.240, L.241
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:G.239, B:L.241
- Water bridges: B:G.239
NA.38: 5 residues within 4Å:- Chain B: D.153, D.156, R.157
- Chain C: A.339
- Ligands: EDO.25
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:D.156, B:D.156, B:R.157, B:R.157
NA.56: 4 residues within 4Å:- Chain C: L.236, G.239, K.240, L.241
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:G.239, C:L.241
- Water bridges: C:G.239
NA.57: 5 residues within 4Å:- Chain B: A.339
- Chain C: D.153, D.156, R.157
- Ligands: EDO.44
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:D.153, C:D.153, C:R.157, C:R.157
NA.75: 4 residues within 4Å:- Chain D: L.236, G.239, K.240, L.241
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:G.239, D:L.241
- Water bridges: D:G.239
NA.76: 5 residues within 4Å:- Chain A: A.339
- Chain D: D.153, D.156, R.157
- Ligands: EDO.63
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:D.153, D:D.153, D:R.157, D:R.157
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Taberman, H. et al., Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both. J.Synchrotron Radiat. (2019)
- Release Date
- 2019-07-17
- Peptides
- Xylose isomerase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.10 Å
- Oligo State
- homo-tetramer
- Ligands
- 48 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 4 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)
- 8 x MN: MANGANESE (II) ION(Non-covalent)
- 8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- 8 x NA: SODIUM ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Taberman, H. et al., Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both. J.Synchrotron Radiat. (2019)
- Release Date
- 2019-07-17
- Peptides
- Xylose isomerase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
A