SMTL ID : 4zbc.1

A dehydrated form of glucose isomerase collected at 100K.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: E.181, E.217, H.220, D.245, D.287 Ligands: GLC.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287 MN.2: 6 residues within 4Å: Chain A: E.217, H.220, N.247, D.255, D.257 Ligands: GLC.7 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.1 MN.3: 5 residues within 4Å: Chain A: T.90, T.91, Y.134, V.135, A.136 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.91, A:V.135, H2O.9 MN.4: 2 residues within 4Å: Chain A: D.150 Ligands: GLC.8 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.150, H2O.1 MN.5: 2 residues within 4Å: Chain A: N.250 Chain C: D.264 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.264, H2O.6, H2O.9, H2O.24, H2O.30 MN.6: 1 residues within 4Å: Chain A: D.9 No protein-ligand interaction detected (PLIP) MN.11: 6 residues within 4Å: Chain B: E.181, E.217, H.220, D.245, D.287 Ligands: GLC.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287 MN.12: 6 residues within 4Å: Chain B: E.217, H.220, N.247, D.255, D.257 Ligands: GLC.16 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.12 MN.13: 2 residues within 4Å: Chain A: D.153 Chain B: A.339 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.339, H2O.3, H2O.9 MN.14: 2 residues within 4Å: Chain B: N.250 Chain D: D.264 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.264, H2O.35, H2O.39, H2O.41 MN.15: 2 residues within 4Å: Chain B: G.138, M.158 No protein-ligand interaction detected (PLIP) MN.20: 6 residues within 4Å: Chain C: E.181, E.217, H.220, D.245, D.287 Ligands: GLC.26 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287 MN.21: 6 residues within 4Å: Chain C: E.217, H.220, N.247, D.255, D.257 Ligands: GLC.26 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 MN.22: 5 residues within 4Å: Chain C: T.90, T.91, Y.134, V.135, A.136 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:T.91, C:V.135, H2O.30 MN.23: 2 residues within 4Å: Chain C: D.150 Ligands: GLC.27 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.150, H2O.22 MN.24: 2 residues within 4Å: Chain A: D.264 Chain C: N.250 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.264, H2O.3, H2O.9, H2O.27, H2O.30 MN.25: 1 residues within 4Å: Chain C: D.9 No protein-ligand interaction detected (PLIP) MN.30: 6 residues within 4Å: Chain D: E.181, E.217, H.220, D.245, D.287 Ligands: GLC.35 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.181, D:E.217, D:D.245, D:D.287 MN.31: 6 residues within 4Å: Chain D: E.217, H.220, N.247, D.255, D.257 Ligands: GLC.35 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.33 MN.32: 2 residues within 4Å: Chain C: D.153 Chain D: A.339 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:A.339, H2O.24, H2O.30 MN.33: 2 residues within 4Å: Chain B: D.264 Chain D: N.250 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.264, H2O.14, H2O.18, H2O.20 MN.34: 2 residues within 4Å: Chain D: G.138, M.158 No protein-ligand interaction detected (PLIP)

8 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.7: 15 residues within 4Å: Chain A: W.16, H.54, T.90, F.94, V.135, W.137, E.181, E.217, H.220, D.245, D.287 Chain D: F.26 Ligands: MN.1, MN.2, FRU.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.90, A:T.90 Water bridges: A:W.16, A:W.137, A:N.215 Salt bridges: A:H.54 GLC.8: 5 residues within 4Å: Chain A: D.150, R.152, D.153, D.156 Ligands: MN.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.152, A:D.156, A:D.156 Water bridges: A:R.152, A:R.152 Salt bridges: A:R.152 GLC.16: 15 residues within 4Å: Chain B: W.16, H.54, T.90, F.94, V.135, W.137, E.181, E.217, H.220, D.245, D.287 Chain C: F.26 Ligands: MN.11, MN.12, GLC.17 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:H.54, B:E.181, B:E.181 Water bridges: B:W.137, B:N.215, B:D.245, B:D.255, B:D.287 Salt bridges: B:H.54 GLC.17: 8 residues within 4Å: Chain B: W.16, D.57, F.94, T.95, K.289 Chain C: P.25, F.26 Ligands: GLC.16 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.92, B:T.95, B:K.289, C:P.25 Water bridges: B:D.57, B:T.95 Salt bridges: B:H.54 GLC.26: 15 residues within 4Å: Chain B: F.26 Chain C: W.16, H.54, T.90, F.94, V.135, W.137, E.181, E.217, H.220, D.245, D.287 Ligands: MN.20, MN.21, FRU.29 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.90, C:T.90 Water bridges: C:W.16, C:W.137, C:N.215 Salt bridges: C:H.54 GLC.27: 5 residues within 4Å: Chain C: D.150, R.152, D.153, D.156 Ligands: MN.23 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.152, C:D.156, C:D.156 Water bridges: C:R.152, C:R.152 Salt bridges: C:R.152 GLC.35: 15 residues within 4Å: Chain A: F.26 Chain D: W.16, H.54, T.90, F.94, V.135, W.137, E.181, E.217, H.220, D.245, D.287 Ligands: MN.30, MN.31, GLC.36 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:H.54, D:E.181, D:E.181 Water bridges: D:W.137, D:N.215, D:D.245, D:D.255, D:D.287 Salt bridges: D:H.54 GLC.36: 8 residues within 4Å: Chain A: P.25, F.26 Chain D: W.16, D.57, F.94, T.95, K.289 Ligands: GLC.35 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain D Hydrogen bonds: A:P.25, D:N.92, D:T.95, D:K.289 Water bridges: D:D.57, D:T.95 Salt bridges: D:H.54

8 x FRU: beta-D-fructofuranose(Non-covalent)

FRU.9: 10 residues within 4Å: Chain A: W.20, D.24, P.25, Y.254, D.255, Q.256, K.289, P.291 Chain D: P.25, P.187 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.256, A:Q.256 Water bridges: A:Y.254, A:D.255, A:K.289 FRU.10: 12 residues within 4Å: Chain A: W.16, R.23, H.54, D.57, N.92, F.94, T.95, K.289 Chain D: P.25, F.26, G.27 Ligands: GLC.7 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.23, A:H.54, A:N.92, A:T.95, A:K.289, A:K.289 Water bridges: A:W.16, A:K.289 FRU.18: 10 residues within 4Å: Chain B: W.20, D.24, P.25, Y.254, D.255, Q.256, K.289, P.291 Chain C: P.25, P.187 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.24, B:D.24 Water bridges: B:D.255, B:D.255, B:K.289 FRU.19: 3 residues within 4Å: Chain B: S.64, S.66, E.67 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.64 FRU.28: 10 residues within 4Å: Chain B: P.25, P.187 Chain C: W.20, D.24, P.25, Y.254, D.255, Q.256, K.289, P.291 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.256, C:Q.256 Water bridges: C:Y.254, C:D.255, C:K.289 FRU.29: 12 residues within 4Å: Chain B: P.25, F.26, G.27 Chain C: W.16, R.23, H.54, D.57, N.92, F.94, T.95, K.289 Ligands: GLC.26 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.23, C:H.54, C:N.92, C:T.95, C:K.289, C:K.289 Water bridges: C:W.16, C:K.289 FRU.37: 10 residues within 4Å: Chain A: P.25, P.187 Chain D: W.20, D.24, P.25, Y.254, D.255, Q.256, K.289, P.291 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.24, D:D.24 Water bridges: D:D.255, D:D.255, D:K.289 FRU.38: 3 residues within 4Å: Chain D: S.64, S.66, E.67 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lobley, C.M. et al., A generic protocol for protein crystal dehydration using the HC1b humidity controller. Acta Crystallogr D Struct Biol (2016)

Release Date

2016-03-23

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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