SMTL ID : 4e3v.1

Crystal Structure of XYLOSE ISOMERASE FROM STREPTOMYCES RUBIGINOSUS Cryoprotected in Proline

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

4 x PRO: PROLINE(Non-covalent)

PRO.1: 5 residues within 4Å: Chain A: L.236, A.278, G.279, Y.280, S.281 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:L.236 Hydrogen bonds: A:S.281, P.1, P.1 PRO.6: 5 residues within 4Å: Chain B: L.236, A.278, G.279, Y.280, S.281 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:L.236 Hydrogen bonds: B:S.281, P.6, P.6 PRO.11: 5 residues within 4Å: Chain C: L.236, A.278, G.279, Y.280, S.281 4 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain C Hydrogen bonds: P.11, P.11, C:S.281 Hydrophobic interactions: C:L.236 PRO.16: 5 residues within 4Å: Chain D: L.236, A.278, G.279, Y.280, S.281 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:L.236 Hydrogen bonds: D:S.281, P.16, P.16

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

SO4.2: 4 residues within 4Å: Chain A: W.20, Q.21, G.22, R.23 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.21, A:G.22, A:R.23 Water bridges: A:G.19, A:W.20, A:R.23, A:R.23, A:R.23 Salt bridges: A:R.23 SO4.3: 3 residues within 4Å: Chain A: R.23, D.28, A.29 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.29 Salt bridges: A:R.23 SO4.7: 4 residues within 4Å: Chain B: W.20, Q.21, G.22, R.23 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.21, B:G.22, B:R.23 Water bridges: B:G.19, B:W.20, B:R.23, B:R.23, B:R.23 Salt bridges: B:R.23 SO4.8: 3 residues within 4Å: Chain B: R.23, D.28, A.29 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.29 Salt bridges: B:R.23 SO4.12: 4 residues within 4Å: Chain C: W.20, Q.21, G.22, R.23 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Q.21, C:G.22, C:R.23 Water bridges: C:G.19, C:W.20, C:R.23, C:R.23, C:R.23 Salt bridges: C:R.23 SO4.13: 3 residues within 4Å: Chain C: R.23, D.28, A.29 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.29 Salt bridges: C:R.23 SO4.17: 4 residues within 4Å: Chain D: W.20, Q.21, G.22, R.23 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:Q.21, D:G.22, D:R.23 Water bridges: D:G.19, D:W.20, D:R.23, D:R.23, D:R.23 Salt bridges: D:R.23 SO4.18: 3 residues within 4Å: Chain D: R.23, D.28, A.29 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.29 Salt bridges: D:R.23

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: E.181, E.217, D.245, D.287 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.217, A:D.245, A:D.287, H2O.12, H2O.12 MG.9: 4 residues within 4Å: Chain B: E.181, E.217, D.245, D.287 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.217, B:D.245, B:D.287, H2O.25, H2O.25 MG.14: 4 residues within 4Å: Chain C: E.181, E.217, D.245, D.287 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.217, C:D.245, C:D.287, H2O.37, H2O.37 MG.19: 4 residues within 4Å: Chain D: E.181, E.217, D.245, D.287 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.217, D:D.245, D:D.287, H2O.50, H2O.50

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.5: 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:H.220, A:D.255, A:D.255, A:D.257, H2O.12 MN.10: 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:H.220, B:D.255, B:D.255, B:D.257, H2O.25 MN.15: 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:H.220, C:D.255, C:D.255, C:D.257, H2O.37 MN.20: 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:H.220, D:D.255, D:D.255, D:D.257, H2O.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pemberton, T.A. et al., Proline: Mother Nature's cryoprotectant applied to protein crystallography. Acta Crystallogr.,Sect.D (2012)

Release Date

2012-07-25

Peptides

Xylose isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Xylose isomerase

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