SMTL ID : 5nh4.1

Crystal structure of xylose isomerase from Piromyces E2 in complex with one Mg2+ ions and glycerol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: E.233, E.269, D.297, D.340 Ligands: GOL.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.233, A:E.269, A:D.297, A:D.340 MG.5: 5 residues within 4Å: Chain B: E.233, E.269, D.297, D.340 Ligands: GOL.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.233, B:E.269, B:D.297, B:D.340 MG.13: 5 residues within 4Å: Chain C: E.233, E.269, D.297, D.340 Ligands: GOL.16 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.233, C:E.269, C:D.297, C:D.340 MG.17: 5 residues within 4Å: Chain D: E.233, E.269, D.297, D.340 Ligands: GOL.18 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.233, D:E.269, D:D.297, D:D.340

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: S.112, I.113 Chain B: G.417, E.418 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.113 Water bridges: A:R.166, B:E.418 SO4.6: 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:E.418, A:E.418 SO4.14: 4 residues within 4Å: Chain C: G.417, E.418 Chain D: S.112, I.113 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Water bridges: C:G.417, C:G.417, C:E.418, D:R.166 Hydrogen bonds: D:I.113

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: W.50, H.102, W.140, W.189, E.233, E.269, H.272, D.297, D.340 Ligands: MG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.272 Water bridges: A:T.142, A:W.189 GOL.4: 3 residues within 4Å: Chain A: E.249, K.256 Chain B: A.257 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.249, A:K.256 Water bridges: A:K.256 GOL.7: 10 residues within 4Å: Chain B: W.50, H.102, W.140, W.189, E.233, E.269, H.272, D.297, D.340 Ligands: MG.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.102, B:E.233, B:H.272 GOL.8: 4 residues within 4Å: Chain A: K.207, F.254, A.257 Chain B: E.249 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.249 Water bridges: A:H.258 GOL.9: 5 residues within 4Å: Chain A: K.384, K.385, Y.388 Chain B: D.202, R.205 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.384, B:R.205, B:R.205 Water bridges: A:K.385 GOL.10: 3 residues within 4Å: Chain B: D.29, E.31, K.32 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.29 GOL.11: 5 residues within 4Å: Chain B: Q.8, I.9, Q.10, N.21, L.23 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.10, B:Q.10, B:N.21, B:N.21 GOL.12: 9 residues within 4Å: Chain B: H.26, Y.27, Q.316, D.362, A.363, R.366 Chain C: A.434, M.435, Q.437 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:H.26, B:Q.316, B:R.366, C:A.434, C:Q.437 GOL.15: 3 residues within 4Å: Chain C: E.249, K.256 Chain D: A.257 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.249 Water bridges: C:G.253, C:K.256 GOL.16: 9 residues within 4Å: Chain C: H.102, W.140, W.189, E.233, E.269, H.272, D.297, D.340 Ligands: MG.13 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.102, C:H.272 Water bridges: C:T.142 GOL.18: 10 residues within 4Å: Chain D: W.50, H.102, W.140, W.189, E.233, E.269, H.272, D.297, D.340 Ligands: MG.17 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.102, D:E.233, D:D.340

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
A

B
B

C
C

D
D

Xylose isomerase

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