SMTL ID : 7e9w.1

The Crystal Structure of D-psicose-3-epimerase from Biortus.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: E.173, D.206, H.232, E.267 Ligands: GOL.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.173, A:D.206, A:H.232, A:E.267 MN.5: 5 residues within 4Å: Chain B: E.173, D.206, H.232, E.267 Ligands: GOL.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.173, B:D.206, B:H.232, B:E.267 MN.9: 5 residues within 4Å: Chain C: E.173, D.206, H.232, E.267 Ligands: GOL.12 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.173, C:D.206, C:H.232, C:E.267, H2O.15 MN.13: 5 residues within 4Å: Chain D: E.173, D.206, H.232, E.267 Ligands: GOL.16 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.173, D:D.206, D:H.232, D:E.267

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: N.237, K.239, R.284, I.286, N.288 Chain D: T.185, E.213, D.215 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:N.237, A:K.239, A:R.284, A:R.284, A:N.288, A:N.288, D:E.213 Water bridges: D:D.215 GOL.3: 8 residues within 4Å: Chain A: Y.29, W.37, A.59, G.88, H.89, G.90, W.135 Ligands: GOL.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.29, A:G.90 Water bridges: A:A.60, A:H.89, A:H.89 GOL.4: 9 residues within 4Å: Chain A: W.135, E.173, E.179, D.206, H.209, R.238, E.267 Ligands: MN.1, GOL.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.179, A:R.238, A:R.238 GOL.6: 8 residues within 4Å: Chain B: N.237, K.239, R.284, I.286, N.288 Chain C: T.185, E.213, D.215 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.237, B:K.239, B:R.284, B:R.284, B:N.288, B:N.288, C:E.213 Water bridges: C:D.215 GOL.7: 9 residues within 4Å: Chain B: Y.29, W.37, A.59, S.61, G.88, H.89, G.90, W.135 Ligands: GOL.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.29, B:S.61, B:G.88, B:G.90, B:G.90 Water bridges: B:A.60 GOL.8: 9 residues within 4Å: Chain B: E.173, L.175, E.179, D.206, H.209, R.238, E.267 Ligands: MN.5, GOL.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.179, B:R.238, B:R.238 GOL.10: 7 residues within 4Å: Chain B: T.185, E.213, D.215 Chain C: N.237, K.239, R.284, I.286 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.237, C:K.239, C:R.284, C:I.286, B:E.213 GOL.11: 7 residues within 4Å: Chain C: Y.29, W.37, A.59, G.88, H.89, G.90 Ligands: GOL.12 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.29, C:G.90 Water bridges: C:A.60, C:G.88, C:H.89 GOL.12: 10 residues within 4Å: Chain C: E.173, E.179, D.206, H.209, R.238, E.267, F.269, I.280 Ligands: MN.9, GOL.11 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.179, C:R.238, C:R.238 Water bridges: C:H.232 GOL.14: 8 residues within 4Å: Chain A: T.185, E.213, D.215 Chain D: N.237, K.239, R.284, I.286, N.288 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:N.237, D:K.239, D:R.284, D:R.284, D:N.288, D:N.288, A:E.213 GOL.15: 7 residues within 4Å: Chain D: Y.29, W.37, A.59, G.88, H.89, G.90 Ligands: GOL.16 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.90 Water bridges: D:Y.29, D:G.88, D:H.89 GOL.16: 9 residues within 4Å: Chain D: E.173, E.179, D.206, H.209, R.238, E.267, F.269 Ligands: MN.13, GOL.15 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.179, D:H.209, D:R.238, D:R.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, F. et al., The Crystal Structure of D-psicose-3-epimerase from Biortus. To Be Published

Release Date

2021-03-24

Peptides

D-psicose 3-epimerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

D-psicose 3-epimerase