SMTL ID : 5vr0.1

Crystal structure of glucose isomerase from Streptomyces rubiginosus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

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

MRD.1: 6 residues within 4Å: Chain A: W.16, H.54, D.57, F.94, T.95 Chain C: F.26 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:W.16, A:F.94 Water bridges: A:N.92, C:D.28 MRD.19: 6 residues within 4Å: Chain B: W.16, H.54, D.57, F.94, T.95 Chain D: F.26 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:W.16, B:F.94 Water bridges: B:N.92, D:D.28 MRD.37: 6 residues within 4Å: Chain A: F.26 Chain C: W.16, H.54, D.57, F.94, T.95 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:W.16, C:F.94 Hydrogen bonds: C:T.95 Water bridges: C:N.92, A:D.28 MRD.55: 6 residues within 4Å: Chain B: F.26 Chain D: W.16, H.54, D.57, F.94, T.95 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:W.16, D:F.94 Hydrogen bonds: D:T.95 Water bridges: D:N.92, B:D.28

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

MN.2: 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:E.217, A:H.220, A:D.255, A:D.257, H2O.18 MN.3: 4 residues within 4Å: Chain A: E.181, E.217, D.245, D.287 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287, H2O.10, H2O.10 MN.20: 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:E.217, B:H.220, B:D.255, B:D.257, H2O.36 MN.21: 4 residues within 4Å: Chain B: E.181, E.217, D.245, D.287 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287, H2O.28, H2O.29 MN.38: 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:E.217, C:H.220, C:D.255, C:D.257, H2O.55 MN.39: 4 residues within 4Å: Chain C: E.181, E.217, D.245, D.287 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287, H2O.47, H2O.47 MN.56: 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:E.217, D:H.220, D:D.255, D:D.257, H2O.74 MN.57: 4 residues within 4Å: Chain D: E.181, E.217, D.245, D.287 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.181, D:E.217, D:D.245, D:D.287, H2O.66, H2O.66

48 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: E.204, P.209, E.210, K.240 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain A: Q.234, W.237, A.238 Chain D: A.201, F.202, R.205 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: L.236, G.239, K.240, L.241 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain A: E.294, D.295, G.298 Chain B: G.369, M.370, A.371 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: D.28, A.29 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: R.109 Ligands: CA.18 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: D.9, F.11, R.284, Y.310 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain A: R.32 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: T.30, R.31, R.292, E.294, D.295 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: R.266, A.267, W.270 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: N.250, A.262, G.263 Chain B: R.266 Ligand excluded by PLIP CL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain B: E.204, P.209, E.210, K.240 Ligand excluded by PLIP CL.23: 6 residues within 4Å: Chain B: Q.234, W.237, A.238 Chain C: A.201, F.202, R.205 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: L.236, G.239, K.240, L.241 Ligand excluded by PLIP CL.25: 6 residues within 4Å: Chain A: G.369, M.370, A.371 Chain B: E.294, D.295, G.298 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain B: D.28, A.29 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain B: R.109 Ligands: CA.36 Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain B: D.9, F.11, R.284, Y.310 Ligand excluded by PLIP CL.29: 1 residues within 4Å: Chain B: R.32 Ligand excluded by PLIP CL.30: 5 residues within 4Å: Chain B: T.30, R.31, R.292, E.294, D.295 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain B: R.266, A.267, W.270 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain A: R.266 Chain B: N.250, A.262, G.263 Ligand excluded by PLIP CL.33: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.40: 4 residues within 4Å: Chain C: E.204, P.209, E.210, K.240 Ligand excluded by PLIP CL.41: 6 residues within 4Å: Chain B: A.201, F.202, R.205 Chain C: Q.234, W.237, A.238 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain C: L.236, G.239, K.240, L.241 Ligand excluded by PLIP CL.43: 6 residues within 4Å: Chain C: E.294, D.295, G.298 Chain D: G.369, M.370, A.371 Ligand excluded by PLIP CL.44: 2 residues within 4Å: Chain C: D.28, A.29 Ligand excluded by PLIP CL.45: 2 residues within 4Å: Chain C: R.109 Ligands: CA.54 Ligand excluded by PLIP CL.46: 4 residues within 4Å: Chain C: D.9, F.11, R.284, Y.310 Ligand excluded by PLIP CL.47: 1 residues within 4Å: Chain C: R.32 Ligand excluded by PLIP CL.48: 5 residues within 4Å: Chain C: T.30, R.31, R.292, E.294, D.295 Ligand excluded by PLIP CL.49: 3 residues within 4Å: Chain C: R.266, A.267, W.270 Ligand excluded by PLIP CL.50: 4 residues within 4Å: Chain C: N.250, A.262, G.263 Chain D: R.266 Ligand excluded by PLIP CL.51: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.58: 4 residues within 4Å: Chain D: E.204, P.209, E.210, K.240 Ligand excluded by PLIP CL.59: 6 residues within 4Å: Chain A: A.201, F.202, R.205 Chain D: Q.234, W.237, A.238 Ligand excluded by PLIP CL.60: 4 residues within 4Å: Chain D: L.236, G.239, K.240, L.241 Ligand excluded by PLIP CL.61: 6 residues within 4Å: Chain C: G.369, M.370, A.371 Chain D: E.294, D.295, G.298 Ligand excluded by PLIP CL.62: 2 residues within 4Å: Chain D: D.28, A.29 Ligand excluded by PLIP CL.63: 2 residues within 4Å: Chain D: R.109 Ligands: CA.72 Ligand excluded by PLIP CL.64: 4 residues within 4Å: Chain D: D.9, F.11, R.284, Y.310 Ligand excluded by PLIP CL.65: 1 residues within 4Å: Chain D: R.32 Ligand excluded by PLIP CL.66: 5 residues within 4Å: Chain D: T.30, R.31, R.292, E.294, D.295 Ligand excluded by PLIP CL.67: 3 residues within 4Å: Chain D: R.266, A.267, W.270 Ligand excluded by PLIP CL.68: 4 residues within 4Å: Chain C: R.266 Chain D: N.250, A.262, G.263 Ligand excluded by PLIP CL.69: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

12 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.16: 2 residues within 4Å: Chain A: D.295, D.297 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.295, A:D.297 CA.17: 1 residues within 4Å: Chain A: A.339 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:A.339, H2O.7, H2O.8, H2O.9, H2O.76 CA.18: 1 residues within 4Å: Ligands: CL.9 No protein-ligand interaction detected (PLIP) CA.34: 2 residues within 4Å: Chain B: D.295, D.297 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.295, B:D.297 CA.35: 1 residues within 4Å: Chain B: A.339 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:A.339, H2O.26, H2O.27, H2O.28, H2O.57 CA.36: 1 residues within 4Å: Ligands: CL.27 No protein-ligand interaction detected (PLIP) CA.52: 2 residues within 4Å: Chain C: D.295, D.297 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.295, C:D.297 CA.53: 1 residues within 4Å: Chain C: A.339 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:A.339, H2O.38, H2O.45, H2O.46, H2O.47 CA.54: 1 residues within 4Å: Ligands: CL.45 No protein-ligand interaction detected (PLIP) CA.70: 2 residues within 4Å: Chain D: D.295, D.297 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.295, D:D.297 CA.71: 1 residues within 4Å: Chain D: A.339 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:A.339, H2O.19, H2O.64, H2O.65, H2O.66 CA.72: 1 residues within 4Å: Ligands: CL.63 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borek, D. et al., Real-space analysis of radiation-induced specific changes with independent component analysis. J Synchrotron Radiat (2018)

Release Date

2018-05-02

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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