SMTL ID : 4hhl.1

High resolution crystal structure of Glucose Isomerase from Streptomyces sp. SK

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-tetramer

Ligands

4 x CO: COBALT (II) ION(Non-covalent)

CO.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.8 CO.12: 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.14 CO.19: 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.22 CO.30: 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.28

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 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.3, H2O.5 MG.3: 3 residues within 4Å: Chain A: E.67, H.71 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.67, A:H.71 MG.13: 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.10, H2O.13 MG.20: 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.17, H2O.19 MG.21: 3 residues within 4Å: Chain C: E.67, H.71 Ligands: EDO.23 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.67, C:H.71 MG.31: 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.24, H2O.27

26 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 7 residues within 4Å: Chain A: L.258, R.259, P.291 Chain C: E.373, D.376 Chain D: E.144, S.145 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: E.67, A.70, H.71, R.74 Ligands: MG.3 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: R.321, L.330 Chain B: G.146, A.147, K.149, D.150 Ligands: EDO.16 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: A.201, F.202, R.205 Chain B: L.200, Q.234, W.237, A.238 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: R.42, E.45, L.46, W.300 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain A: D.56, F.61, N.92, F.94, T.95, H.96, F.99, K.118 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: P.36, V.37, L.58, H.71, R.74 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain A: R.334, A.365, R.368, M.370 Chain B: P.97, V.98, K.100, D.108 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: R.117 Chain B: L.351, A.352, D.353, R.354, E.358 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain B: L.236, G.239, K.240, L.241, W.280 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: D.273, L.274, S.277, R.321 Chain B: D.150, R.152 Ligands: EDO.6 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: H.230, G.231, Q.234 Chain B: L.192, L.193, P.194, H.198 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: D.108, R.109, D.110 Chain B: Q.337, R.368 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain A: E.373, D.376 Chain B: E.144, S.145 Chain C: L.258, R.259, P.291 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain C: E.67, A.70, H.71, R.74 Ligands: MG.21 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain C: R.321, L.330 Chain D: G.146, A.147, K.149, D.150 Ligands: EDO.34 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain C: A.201, F.202, R.205 Chain D: L.200, Q.234, W.237, A.238 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain C: R.42, E.45, L.46, W.300 Ligand excluded by PLIP EDO.27: 8 residues within 4Å: Chain C: D.56, F.61, N.92, F.94, T.95, H.96, F.99, K.118 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain C: P.36, V.37, L.58, H.71, R.74 Ligand excluded by PLIP EDO.29: 8 residues within 4Å: Chain C: R.334, A.365, R.368, M.370 Chain D: P.97, V.98, K.100, D.108 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain C: R.117 Chain D: L.351, A.352, D.353, R.354, E.358 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain D: L.236, G.239, K.240, L.241, W.280 Ligand excluded by PLIP EDO.34: 7 residues within 4Å: Chain C: D.273, L.274, S.277, R.321 Chain D: D.150, R.152 Ligands: EDO.24 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain C: H.230, G.231, Q.234 Chain D: L.192, L.193, P.194, H.198 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain C: D.108, R.109, D.110 Chain D: Q.337, R.368 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ben Hlima, H. et al., Identification of critical residues for the activity and thermostability of Streptomyces sp. SK glucose isomerase. Appl.Microbiol.Biotechnol. (2013)

Release Date

2013-03-27

Peptides

Xylose isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Xylose isomerase