SMTL ID : 4gik.1

Crystal Structure of Pseudouridine Monophosphate Glycosidase/Linear R5P Adduct

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-trimer

Ligands

3 x R5P: RIBOSE-5-PHOSPHATE(Post Translational Modification)

R5P.1: 12 residues within 4Å: Chain A: E.54, T.56, K.116, T.135, V.136, G.155, G.157, S.170, D.172, K.189, K.290, T.293 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:K.189 Hydrogen bonds: A:E.54, A:V.136, A:S.170, A:K.189 Water bridges: A:K.116, A:S.118, A:A.171, A:D.172, A:T.293 Salt bridges: A:K.116 R5P.3: 11 residues within 4Å: Chain B: E.54, T.56, K.116, T.135, V.136, G.155, G.157, S.170, D.172, K.189, T.293 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:K.189 Hydrogen bonds: B:E.54, B:V.136, B:G.157, B:S.170, B:K.189 Water bridges: B:H.160, B:A.171, B:D.172, B:T.293, A:E.202, A:E.202, A:E.202 Salt bridges: B:K.116 R5P.5: 11 residues within 4Å: Chain C: E.54, T.56, K.116, T.135, V.136, G.155, G.157, S.170, D.172, K.189, T.293 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:K.189 Hydrogen bonds: C:E.54, C:V.136, C:G.157, C:K.189, C:T.293 Water bridges: C:K.116, C:H.160, C:S.170, C:A.171, C:A.171, C:D.172 Salt bridges: C:K.116

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

MN.2: 3 residues within 4Å: Chain A: H.160, D.168, G.289 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.168, H2O.5, H2O.5, H2O.5, H2O.6, H2O.13 MN.4: 2 residues within 4Å: Chain A: E.202 Chain B: D.168 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.168, H2O.5, H2O.5, H2O.10, H2O.10, H2O.11 MN.6: 2 residues within 4Å: Chain B: E.202 Chain C: D.168 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:D.168, H2O.10, H2O.12, H2O.13, H2O.13, H2O.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, S. et al., Pseudouridine monophosphate glycosidase: a new glycosidase mechanism. Biochemistry (2012)

Release Date

2012-10-31

Peptides

Pseudouridine-5'-phosphate glycosidase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Pseudouridine-5'-phosphate glycosidase

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