SMTL ID : 6oe8.1

The crystal structure of hyper-thermostable AgUricase mutant K12C/E286C

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-tetramer

Ligands

5 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.1: 7 residues within 4Å: Chain A: P.272, K.274, A.296, D.297, Y.300 Chain C: R.298 Ligands: MLI.15 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.274, A:K.274 PG4.4: 2 residues within 4Å: Chain A: L.278, N.288 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.290 PG4.6: 4 residues within 4Å: Chain B: K.274, D.297, Y.300 Chain D: R.298 No protein-ligand interaction detected (PLIP) PG4.12: 7 residues within 4Å: Chain A: R.298 Chain C: P.272, K.274, A.296, D.297, Y.300 Ligands: MLI.17 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.297 Water bridges: C:K.274 PG4.19: 7 residues within 4Å: Chain B: R.298 Chain D: P.272, K.274, A.296, D.297, Y.300 Ligands: MLI.10 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.297

8 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 7 residues within 4Å: Chain A: K.95, N.96, Y.99 Chain B: V.279, D.280, Y.294 Chain D: P.299 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.95, B:D.280 Water bridges: B:D.280 PGE.3: 8 residues within 4Å: Chain A: E.48, N.67, T.69, A.133, A.134, Q.135, T.158, R.213 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.69, A:R.213, A:R.213 Water bridges: A:R.131 PGE.7: 6 residues within 4Å: Chain A: V.279 Chain B: D.92, K.95, N.96, Y.99 Chain C: F.277 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Water bridges: C:T.197 Hydrogen bonds: B:D.92, B:K.95 PGE.8: 8 residues within 4Å: Chain B: E.48, N.67, T.69, A.133, A.134, Q.135, T.158, R.213 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.69, B:R.213, B:R.213 PGE.13: 7 residues within 4Å: Chain B: H.275, F.277, P.299 Chain C: K.46, K.95, Y.99 Chain D: Y.294 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.46, C:K.95 Water bridges: C:K.46 PGE.14: 9 residues within 4Å: Chain C: E.48, N.67, T.69, A.133, A.134, Q.135, T.158, A.159, R.213 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.213, C:R.213 Water bridges: C:T.69, B:Y.300 PGE.16: 6 residues within 4Å: Chain C: V.279, D.280, F.284 Chain D: K.95, N.96, Y.99 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.95 Water bridges: D:N.96, C:Y.294 PGE.20: 8 residues within 4Å: Chain D: E.48, N.67, T.69, A.133, A.134, Q.135, T.158, R.213 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:T.69, D:R.213, D:R.213 Water bridges: A:Y.300

8 x MLI: MALONATE ION(Non-functional Binders)

MLI.5: 8 residues within 4Å: Chain A: A.90, T.91, D.92 Chain D: F.187, L.198, R.204, N.273, H.275 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:F.187 Hydrogen bonds: D:N.273, A:T.91, A:T.91, A:D.92 Water bridges: D:R.204, A:K.46, A:K.46 Salt bridges: D:R.204, D:H.275, A:K.46 MLI.9: 8 residues within 4Å: Chain B: A.90, T.91, D.92 Chain C: F.187, L.198, R.204, N.273, H.275 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:T.91, B:T.91, B:D.92, C:N.273 Water bridges: B:K.46, B:T.91, C:R.204 Salt bridges: B:K.46, C:R.204, C:H.275 Hydrophobic interactions: C:F.187, C:L.198 MLI.10: 5 residues within 4Å: Chain B: R.298 Chain C: R.50, F.137, R.151 Ligands: PG4.19 12 PLIP interactions: 2 interactions with chain D, 9 interactions with chain C, 1 interactions with chain B Water bridges: D:K.274, D:D.297, C:R.50, C:R.50, C:R.50, C:R.50, C:N.67, C:R.151 Hydrophobic interactions: C:F.137 Salt bridges: C:R.50, C:R.151, B:R.298 MLI.11: 8 residues within 4Å: Chain B: F.187, L.198, R.204, N.273, H.275 Chain C: A.90, T.91, D.92 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:F.187 Hydrogen bonds: B:N.273, C:T.91, C:T.91, C:T.91, C:D.92 Water bridges: B:R.204, C:K.46, C:K.46 Salt bridges: B:R.204, B:H.275 MLI.15: 6 residues within 4Å: Chain B: R.50, N.67, F.137, R.151 Chain C: R.298 Ligands: PG4.1 12 PLIP interactions: 1 interactions with chain C, 11 interactions with chain B Salt bridges: C:R.298, B:R.50, B:R.50, B:R.151 Hydrophobic interactions: B:F.137 Water bridges: B:R.50, B:R.50, B:R.50, B:N.67, B:R.151, B:R.151, B:R.151 MLI.17: 6 residues within 4Å: Chain A: R.298 Chain D: R.50, N.67, F.137, R.151 Ligands: PG4.12 13 PLIP interactions: 2 interactions with chain C, 10 interactions with chain D, 1 interactions with chain A Water bridges: C:K.274, C:D.297, D:R.50, D:N.67, D:R.151, D:R.151, D:R.151, D:R.151 Hydrophobic interactions: D:F.137 Salt bridges: D:R.50, D:R.50, D:R.151, A:R.298 MLI.18: 8 residues within 4Å: Chain A: F.187, L.198, R.204, N.273, H.275 Chain D: A.90, T.91, D.92 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: A:F.187, A:L.198 Hydrogen bonds: A:N.273, D:T.91, D:T.91, D:D.92 Water bridges: A:R.204, A:R.204, D:K.46, D:T.91 Salt bridges: A:R.204, A:H.275, D:K.46 MLI.21: 5 residues within 4Å: Chain A: R.50, N.67, F.137, R.151 Chain D: R.298 12 PLIP interactions: 10 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: A:F.137 Water bridges: A:R.50, A:R.50, A:R.50, A:R.50, A:N.67, A:R.151, B:K.274 Salt bridges: A:R.50, A:R.50, A:R.151, D:R.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, Y. et al., Structure-based design of a hyperthermostable AgUricase for hyperuricemia and gout therapy. Acta Pharmacol.Sin. (2019)

Release Date

2019-08-21

Peptides

Uricase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Uricase