SMTL ID : 4us6.1

New Crystal Form of Glucose Isomerase Grown in Short Peptide Supramolecular Hydrogels

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 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.13 CA.8: 6 residues within 4Å: Chain B: E.217, H.220, N.247, D.255, D.257 Ligands: GOL.10 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.31 CA.14: 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.49 CA.21: 6 residues within 4Å: Chain D: E.217, H.220, N.247, D.255, D.257 Ligands: GOL.23 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.67

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: E.181, E.217, H.220, D.245, D.287 Ligands: GOL.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287 MG.7: 1 residues within 4Å: Chain A: D.150 No protein-ligand interaction detected (PLIP) MG.9: 6 residues within 4Å: Chain B: E.181, E.217, H.220, D.245, D.287 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287 MG.15: 6 residues within 4Å: Chain C: E.181, E.217, H.220, D.245, D.287 Ligands: GOL.16 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287 MG.20: 1 residues within 4Å: Chain C: D.150 No protein-ligand interaction detected (PLIP) MG.22: 6 residues within 4Å: Chain D: E.181, E.217, H.220, D.245, D.287 Ligands: GOL.23 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.181, D:E.217, D:D.245, D:D.287

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 13 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 Ligands: MG.2, GOL.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:H.54, A:D.287, A:D.287 Water bridges: A:T.90, A:T.91, A:N.215, A:H.220, A:H.220 GOL.4: 11 residues within 4Å: Chain A: W.20, D.24, P.25, Y.254, D.255, Q.256, D.257, L.258, K.289 Chain D: P.25, F.26 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.256, A:K.289 Water bridges: A:D.24, A:D.24, A:E.186 GOL.5: 9 residues within 4Å: Chain A: W.16, H.54, F.94, W.137, K.183, H.220, K.289 Chain D: F.26 Ligands: GOL.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.289 Water bridges: A:W.16, A:D.57, A:D.287 GOL.10: 15 residues within 4Å: Chain B: W.16, H.54, T.90, F.94, V.135, W.137, E.181, N.215, E.217, H.220, D.245, D.287 Ligands: CA.8, MG.9, GOL.11 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.54, B:E.181, B:D.287 Water bridges: B:T.90, B:T.90, B:N.215, B:H.220, B:H.220 GOL.11: 9 residues within 4Å: Chain B: W.16, H.54, F.94, W.137, K.183, H.220, K.289 Chain C: F.26 Ligands: GOL.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.289 Water bridges: B:D.257, B:D.257 GOL.12: 11 residues within 4Å: Chain B: W.20, D.24, P.25, Y.254, D.255, Q.256, D.257, L.258, K.289 Chain C: P.25 Ligands: NA.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.255, B:Q.256, B:K.289 GOL.16: 13 residues within 4Å: 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: MG.15, GOL.18 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:H.54, C:D.287, C:D.287 Water bridges: C:T.90, C:T.91, C:N.215, C:H.220, C:H.220 GOL.17: 11 residues within 4Å: Chain B: P.25, F.26 Chain C: W.20, D.24, P.25, Y.254, D.255, Q.256, D.257, L.258, K.289 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.256, C:K.289 Water bridges: C:D.24, C:D.24, C:E.186 GOL.18: 9 residues within 4Å: Chain B: F.26 Chain C: W.16, H.54, F.94, W.137, K.183, H.220, K.289 Ligands: GOL.16 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.289 Water bridges: C:W.16, C:D.57, C:D.287 GOL.23: 15 residues within 4Å: Chain D: W.16, H.54, T.90, F.94, V.135, W.137, E.181, N.215, E.217, H.220, D.245, D.287 Ligands: CA.21, MG.22, GOL.24 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:H.54, D:E.181, D:D.287 Water bridges: D:T.90, D:T.90, D:N.215, D:H.220, D:H.220 GOL.24: 9 residues within 4Å: Chain A: F.26 Chain D: W.16, H.54, F.94, W.137, K.183, H.220, K.289 Ligands: GOL.23 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.289 Water bridges: D:D.257, D:D.257 GOL.25: 11 residues within 4Å: Chain A: P.25 Chain D: W.20, D.24, P.25, Y.254, D.255, Q.256, D.257, L.258, K.289 Ligands: NA.26 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.255, D:Q.256, D:K.289

4 x NA: SODIUM ION(Non-functional Binders)

NA.6: 5 residues within 4Å: Chain A: D.55, D.56, I.59, P.60, F.61 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.56, A:D.56 Water bridges: A:G.62 NA.13: 5 residues within 4Å: Chain B: Y.254, Q.256 Chain C: E.144, P.187 Ligands: GOL.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.187 NA.19: 5 residues within 4Å: Chain C: D.55, D.56, I.59, P.60, F.61 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.55, C:D.56 Water bridges: C:G.62 NA.26: 5 residues within 4Å: Chain A: E.144, P.187 Chain D: Y.254, Q.256 Ligands: GOL.25 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.254

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Conejero-Muriel, M. et al., Influence of the Chirality of Short Peptide Supramolecular Hydrogels in Protein Crystallogenesis. Chem.Commun.(Camb.) (2015)

Release Date

2015-05-13

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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