SMTL ID : 4zb0.1

A dehydrated form of glucose isomerase collected at room temperature.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

20 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.1: 5 residues within 4Å: Chain A: E.180, E.216, D.244, D.286 Ligands: GLC.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.180, A:E.216, A:D.244, A:D.286 MN.2: 1 residues within 4Å: Chain A: D.79 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.79, H2O.5, H2O.7 MN.3: 5 residues within 4Å: Chain A: E.216, H.219, N.246, D.254, D.256 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.216, A:H.219, A:D.254, A:D.256, H2O.2 MN.4: 1 residues within 4Å: Chain A: H.70 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.70 MN.5: 4 residues within 4Å: Chain A: A.200, R.204 Chain B: E.203, A.237 No protein-ligand interaction detected (PLIP) MN.8: 5 residues within 4Å: Chain B: E.180, E.216, D.244, D.286 Ligands: GLC.13 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.180, B:E.216, B:D.244, B:D.286 MN.9: 6 residues within 4Å: Chain B: E.216, H.219, N.246, D.254, D.256 Ligands: GLC.13 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.216, B:H.219, B:D.254, B:D.256, H2O.10 MN.10: 7 residues within 4Å: Chain B: T.5, P.6, R.9, F.10, G.46, A.47, H.48 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.5, B:G.46 MN.11: 6 residues within 4Å: Chain B: D.100, T.104, R.139, E.140, G.141, K.148 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.100, B:T.104 MN.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MN.15: 5 residues within 4Å: Chain C: E.180, E.216, D.244, D.286 Ligands: GLC.20 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.180, C:E.216, C:D.244, C:D.286 MN.16: 1 residues within 4Å: Chain C: D.79 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.79, H2O.22, H2O.24 MN.17: 5 residues within 4Å: Chain C: E.216, H.219, N.246, D.254, D.256 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.216, C:H.219, C:D.254, C:D.256, H2O.19 MN.18: 1 residues within 4Å: Chain C: H.70 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.70 MN.19: 4 residues within 4Å: Chain C: A.200, R.204 Chain D: E.203, A.237 No protein-ligand interaction detected (PLIP) MN.22: 5 residues within 4Å: Chain D: E.180, E.216, D.244, D.286 Ligands: GLC.27 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.180, D:E.216, D:D.244, D:D.286 MN.23: 6 residues within 4Å: Chain D: E.216, H.219, N.246, D.254, D.256 Ligands: GLC.27 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.216, D:H.219, D:D.254, D:D.256, H2O.27 MN.24: 7 residues within 4Å: Chain D: T.5, P.6, R.9, F.10, G.46, A.47, H.48 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.5, D:G.46 MN.25: 6 residues within 4Å: Chain D: D.100, T.104, R.139, E.140, G.141, K.148 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.100, D:T.104 MN.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

GLC.6: 13 residues within 4Å: Chain A: W.15, H.53, T.89, F.93, V.134, W.136, E.180, E.216, H.219, D.244, D.286 Chain D: F.25 Ligands: MN.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.89 Water bridges: A:W.15, A:W.136, A:N.214, A:N.214 Salt bridges: A:H.53 GLC.13: 15 residues within 4Å: Chain B: W.15, H.53, T.89, F.93, V.134, W.136, E.180, E.216, H.219, D.244, D.286, K.288 Chain C: F.25 Ligands: MN.8, MN.9 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.89, B:E.180, B:E.216 Water bridges: B:W.15, B:W.136, B:D.254, B:D.256, B:D.256 Salt bridges: B:H.53 GLC.20: 13 residues within 4Å: Chain B: F.25 Chain C: W.15, H.53, T.89, F.93, V.134, W.136, E.180, E.216, H.219, D.244, D.286 Ligands: MN.15 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:T.89, C:E.216 Water bridges: C:W.15, C:W.136, C:N.214, C:N.214, C:E.216, C:D.254, C:D.254 Salt bridges: C:H.53 GLC.27: 15 residues within 4Å: Chain A: F.25 Chain D: W.15, H.53, T.89, F.93, V.134, W.136, E.180, E.216, H.219, D.244, D.286, K.288 Ligands: MN.22, MN.23 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:T.89, D:E.180, D:E.216 Water bridges: D:W.15, D:W.136, D:D.254, D:D.256, D:D.256 Salt bridges: D:H.53

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

FRU.7: 11 residues within 4Å: Chain A: W.19, D.23, P.24, Y.253, D.254, Q.255, K.288, P.290 Chain D: P.24, E.185, P.186 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.23, A:D.23, A:D.254 Water bridges: A:Q.255, A:K.288 FRU.14: 6 residues within 4Å: Chain A: D.107, R.108, D.109 Chain B: E.336, R.339, R.367 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:E.336, B:E.336, A:D.107, A:R.108, A:D.109, A:D.109 FRU.21: 11 residues within 4Å: Chain B: P.24, E.185, P.186 Chain C: W.19, D.23, P.24, Y.253, D.254, Q.255, K.288, P.290 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.23, C:D.23, C:D.254 Water bridges: C:Q.255, C:K.288 FRU.28: 6 residues within 4Å: Chain C: D.107, R.108, D.109 Chain D: E.336, R.339, R.367 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.107, C:R.108, C:D.109, C:D.109, D:E.336, D:E.336

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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