SMTL ID : 1oad.1

Glucose isomerase from Streptomyces rubiginosus in P21212 crystal form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: E.217, H.220, D.255, D.257 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.217, A:H.220, A:D.255, A:D.257, H2O.18 MN.6: 4 residues within 4Å: Chain B: E.217, H.220, D.255, D.257 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.217, B:H.220, B:D.255, B:D.257, H2O.35 MN.11: 4 residues within 4Å: Chain C: E.217, H.220, D.255, D.257 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.217, C:H.220, C:D.255, C:D.257, H2O.53 MN.16: 4 residues within 4Å: Chain D: E.217, H.220, D.255, D.257 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.217, D:H.220, D:D.255, D:D.257, H2O.70

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: E.181, E.217, D.245, D.287 Ligands: MQD.4 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.13 MG.7: 5 residues within 4Å: Chain B: E.181, E.217, D.245, D.287 Ligands: MQD.9 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.30 MG.12: 5 residues within 4Å: Chain C: E.181, E.217, D.245, D.287 Ligands: MQD.14 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.48 MG.17: 5 residues within 4Å: Chain D: E.181, E.217, D.245, D.287 Ligands: MQD.19 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.65

4 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.3: 7 residues within 4Å: Chain A: P.25, F.26 Chain B: W.16, H.54, D.57, F.94, T.95 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.16, B:F.94 Hydrogen bonds: B:T.95 Water bridges: B:N.92 MRD.8: 6 residues within 4Å: Chain A: W.16, H.54, F.94, T.95 Chain B: P.25, F.26 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.16, A:F.94 Water bridges: A:N.92 MRD.13: 7 residues within 4Å: Chain C: P.25, F.26 Chain D: W.16, H.54, D.57, F.94, T.95 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:W.16, D:F.94 Hydrogen bonds: D:T.95 Water bridges: D:N.92 MRD.18: 6 residues within 4Å: Chain C: W.16, H.54, F.94, T.95 Chain D: P.25, F.26 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.16, C:F.94 Water bridges: C:N.92

4 x MQD: 2-METHYLPENTANE-1,2,4-TRIOL(Non-covalent)

MQD.4: 10 residues within 4Å: Chain A: W.16, H.54, T.90, F.94, W.137, E.181, E.217, H.220, D.287 Ligands: MG.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.16, A:T.90, A:F.94, A:W.137 Water bridges: A:W.16, A:D.257, A:D.257, A:D.287 MQD.9: 11 residues within 4Å: Chain B: W.16, H.54, T.90, F.94, V.135, W.137, E.181, E.217, H.220, D.287 Ligands: MG.7 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.16, B:T.90, B:F.94, B:V.135, B:W.137 Water bridges: B:W.16, B:W.16, B:T.90, B:D.257, B:D.257, B:D.257, B:D.287, B:D.287 MQD.14: 10 residues within 4Å: Chain C: W.16, H.54, T.90, F.94, W.137, E.181, E.217, H.220, D.287 Ligands: MG.12 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.16, C:T.90, C:F.94, C:W.137 Water bridges: C:W.16, C:D.257, C:D.257, C:D.287 MQD.19: 11 residues within 4Å: Chain D: W.16, H.54, T.90, F.94, V.135, W.137, E.181, E.217, H.220, D.287 Ligands: MG.17 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:W.16, D:T.90, D:F.94, D:V.135, D:W.137 Water bridges: D:W.16, D:W.16, D:T.90, D:D.257, D:D.257, D:D.257, D:D.287, D:D.287

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 4 residues within 4Å: Chain A: Y.3, E.315, R.316 Chain D: G.385 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:R.316, D:G.385 Water bridges: A:R.316 TRS.15: 4 residues within 4Å: Chain B: G.385 Chain C: Y.3, E.315, R.316 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:G.385, C:R.316 Water bridges: C:R.316

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.10: 4 residues within 4Å: Chain A: R.331, R.334, D.336, E.337 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.331 Hydrogen bonds: A:D.336, A:E.337 MPD.20: 4 residues within 4Å: Chain C: R.331, R.334, D.336, E.337 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:R.331 Hydrogen bonds: C:D.336, C:E.337

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ramagopal, U.A. et al., Sad Manganese in Two Crystal Forms of Glucose Isomerase. Acta Crystallogr.,Sect.D (2003)

Release Date

2003-01-30

Peptides

XYLOSE ISOMERASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

XYLOSE ISOMERASE

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