SMTL ID : 5nh5.1

Crystal structure of native xylose isomerase from Piromyces E2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 8 residues within 4Å: Chain A: E.233, E.269, H.272, D.297, D.340 Ligands: FE2.2, MG.3, GOL.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.233, A:E.269, A:D.297, A:D.340 CA.11: 8 residues within 4Å: Chain B: E.233, E.269, H.272, D.297, D.340 Ligands: FE2.12, MG.13, GOL.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.233, B:E.269, B:D.297, B:D.340 CA.22: 7 residues within 4Å: Chain C: E.233, E.269, D.297, D.340 Ligands: FE2.23, MG.24, GOL.26 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.233, C:E.269, C:D.297, C:D.340 CA.29: 7 residues within 4Å: Chain D: E.233, E.269, D.297, D.340 Ligands: FE2.30, MG.31, GOL.33 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.233, D:E.269, D:D.297, D:D.340

4 x FE2: FE (II) ION(Non-covalent)

FE2.2: 7 residues within 4Å: Chain A: E.233, E.269, D.297, D.340 Ligands: CA.1, MG.3, GOL.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.233, A:E.269, A:D.297, A:D.340 FE2.12: 7 residues within 4Å: Chain B: E.233, E.269, D.297, D.340 Ligands: CA.11, MG.13, GOL.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.233, B:E.269, B:D.297, B:D.340 FE2.23: 7 residues within 4Å: Chain C: E.233, E.269, D.297, D.340 Ligands: CA.22, MG.24, GOL.26 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.233, C:E.269, C:D.297, C:D.340 FE2.30: 8 residues within 4Å: Chain D: E.233, E.269, H.272, D.297, D.340 Ligands: CA.29, MG.31, GOL.33 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.233, D:E.269, D:D.297, D:D.340

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: E.233, E.269, D.297, D.340 Ligands: CA.1, FE2.2, GOL.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.233, A:E.269, A:D.297, A:D.340 MG.13: 7 residues within 4Å: Chain B: E.233, E.269, D.297, D.340 Ligands: CA.11, FE2.12, GOL.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.233, B:E.269, B:D.297, B:D.340 MG.24: 7 residues within 4Å: Chain C: E.233, E.269, D.297, D.340 Ligands: CA.22, FE2.23, GOL.26 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.233, C:E.269, C:D.297, C:D.340 MG.31: 7 residues within 4Å: Chain D: E.233, E.269, D.297, D.340 Ligands: CA.29, FE2.30, GOL.33 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)

SO4.4: 4 residues within 4Å: Chain A: S.112, I.113 Chain B: G.417, E.418 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:I.113 Water bridges: A:E.114, A:R.166, B:G.417, B:G.417, B:E.418, B:E.418 SO4.14: 4 residues within 4Å: Chain A: G.417, E.418 Chain B: S.112, I.113 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.111, B:I.113 Water bridges: B:E.114, B:R.166, A:G.417, A:E.418 SO4.32: 4 residues within 4Å: Chain C: G.417, E.418 Chain D: S.112, I.113 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Water bridges: C:G.417, C:E.418, D:R.166 Hydrogen bonds: D:I.113

20 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: E.249, I.252, K.256 Chain B: A.257 Ligand excluded by PLIP GOL.6: 8 residues within 4Å: Chain A: H.26, Y.27, Q.316, D.362, R.366 Chain D: A.434, M.435, Q.437 Ligand excluded by PLIP GOL.7: 12 residues within 4Å: Chain A: H.102, W.140, F.146, W.189, E.233, E.269, H.272, D.297, D.340 Ligands: CA.1, FE2.2, MG.3 Ligand excluded by PLIP GOL.8: 5 residues within 4Å: Chain A: Q.8, I.9, Q.10, N.21, L.23 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: D.202, R.205 Chain B: K.384, K.385, Y.388 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain A: P.22, L.23, E.351 Chain D: L.428 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain B: Q.8, I.9, Q.10, N.21, L.23 Ligand excluded by PLIP GOL.16: 10 residues within 4Å: Chain B: H.102, W.140, W.189, E.233, E.269, D.297, D.340 Ligands: CA.11, FE2.12, MG.13 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain A: A.257 Chain B: E.249, I.252, K.256 Ligand excluded by PLIP GOL.18: 3 residues within 4Å: Chain B: P.22, E.351 Chain C: L.428 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain B: E.56, G.64, K.66, S.67 Chain D: K.149 Ligand excluded by PLIP GOL.20: 8 residues within 4Å: Chain B: H.26, Y.27, Q.316, D.362, R.366 Chain C: A.434, M.435, Q.437 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain B: L.120, K.121, V.124, N.173, D.176, A.177, E.180 Ligand excluded by PLIP GOL.25: 4 residues within 4Å: Chain C: I.9, Q.10, N.21, L.23 Ligand excluded by PLIP GOL.26: 11 residues within 4Å: Chain C: H.102, W.140, W.189, E.233, E.269, H.272, D.297, D.340 Ligands: CA.22, FE2.23, MG.24 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain C: E.249, I.252, K.256 Chain D: A.257 Ligand excluded by PLIP GOL.28: 6 residues within 4Å: Chain B: A.434, M.435 Chain C: H.26, Y.27, D.362, R.366 Ligand excluded by PLIP GOL.33: 11 residues within 4Å: Chain D: H.102, W.140, W.189, E.233, E.269, H.272, D.297, D.340 Ligands: CA.29, FE2.30, MG.31 Ligand excluded by PLIP GOL.34: 4 residues within 4Å: Chain D: I.9, Q.10, N.21, L.23 Ligand excluded by PLIP GOL.35: 3 residues within 4Å: Chain C: A.257 Chain D: E.249, K.256 Ligand excluded by PLIP

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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